54993
2019
2019
eng
10
2
postprint
1
2019-12-24
2019-12-24
--
Cell architecture of the giant sulfur bacterium achromatium oxaliferum
Achromatium oxaliferum is a large sulfur bacterium easily recognized by large intracellular calcium carbonate bodies. Although these bodies often fill major parts of the cells' volume, their role and specific intracellular location are unclear. In this study, we used various microscopy and staining techniques to identify the cell compartment harboring the calcium carbonate bodies. We observed that Achromatium cells often lost their calcium carbonate bodies, either naturally or induced by treatments with diluted acids, ethanol, sodium bicarbonate and UV radiation which did not visibly affect the overall shape and motility of the cells (except for UV radiation). The water-soluble fluorescent dye fluorescein easily diffused into empty cavities remaining after calcium carbonate loss. Membranes (stained with Nile Red) formed a network stretching throughout the cell and surrounding empty or filled calcium carbonate cavities. The cytoplasm (stained with FITC and SYBR Green for nucleic acids) appeared highly condensed and showed spots of dissolved Ca2+ (stained with Fura-2). From our observations, we conclude that the calcium carbonate bodies are located in the periplasm, in extra-cytoplasmic pockets of the cytoplasmic membrane and are thus kept separate from the cell's cytoplasm. This periplasmic localization of the carbonate bodies might explain their dynamic formation and release upon environmental changes.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
Extra-cytoplasmic localization of calcium carbonate bodies
urn:nbn:de:kobv:517-opus4-549935
1866-8372
10.25932/publishup-54993
online registration
publish
<a href="http://publishup.uni-potsdam.de/60815">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
false
true
CC-BY - Namensnennung 4.0 International
Sina Schorn
Verena Salman-Carvalho
Sten Littmann
Danny Ionescu
Hans-Peter Grossart
Heribert Cypionka
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1356
eng
uncontrolled
sulfur-bacteria
eng
uncontrolled
calcium carbonate inclusions
eng
uncontrolled
extra-cytoplasmic pockets
eng
uncontrolled
calcite
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/54993/zmnr1356.pdf
60815
2019
2019
eng
1
8
8
2
96
article
Oxford University Press
Oxford
1
2019-12-24
2019-12-24
--
Cell architecture of the giant sulfur bacterium achromatium oxaliferum
Achromatium oxaliferum is a large sulfur bacterium easily recognized by large intracellular calcium carbonate bodies. Although these bodies often fill major parts of the cells' volume, their role and specific intracellular location are unclear. In this study, we used various microscopy and staining techniques to identify the cell compartment harboring the calcium carbonate bodies. We observed that Achromatium cells often lost their calcium carbonate bodies, either naturally or induced by treatments with diluted acids, ethanol, sodium bicarbonate and UV radiation which did not visibly affect the overall shape and motility of the cells (except for UV radiation). The water-soluble fluorescent dye fluorescein easily diffused into empty cavities remaining after calcium carbonate loss. Membranes (stained with Nile Red) formed a network stretching throughout the cell and surrounding empty or filled calcium carbonate cavities. The cytoplasm (stained with FITC and SYBR Green for nucleic acids) appeared highly condensed and showed spots of dissolved Ca2+ (stained with Fura-2). From our observations, we conclude that the calcium carbonate bodies are located in the periplasm, in extra-cytoplasmic pockets of the cytoplasmic membrane and are thus kept separate from the cell's cytoplasm. This periplasmic localization of the carbonate bodies might explain their dynamic formation and release upon environmental changes.
FEMS Microbiology Ecology
Extra-cytoplasmic localization of calcium carbonate bodies
10.1093/femsec/fiz200
1574-6941
fiz200
Schorn, Sina
1501712-6
<a href="https://doi.org/10.25932/publishup-54993">Zweitveröffentlichung in der Schriftenreihe Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1356</a>
false
false
CC-BY - Namensnennung 4.0 International
Sina Schorn
Verena Salman-Carvalho
Sten Littmann
Danny Ionescu
Hans-Peter Grossart
Heribert Cypionka
eng
uncontrolled
sulfur-bacteria
eng
uncontrolled
calcium carbonate inclusions
eng
uncontrolled
extra-cytoplasmic pockets
eng
uncontrolled
calcite
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Hybrid Open-Access
63084
2021
2021
eng
5728
5741
14
10
11
article
Wiley
Hoboken
1
2021-03-29
2021-03-29
--
Movement can mediate temporal mismatches between resource availability and biological events in host-pathogen interactions
Global change is shifting the timing of biological events, leading to temporal mismatches between biological events and resource availability. These temporal mismatches can threaten species' populations. Importantly, temporal mismatches not only exert strong pressures on the population dynamics of the focal species, but can also lead to substantial changes in pairwise species interactions such as host-pathogen systems. We adapted an established individual-based model of host-pathogen dynamics. The model describes a viral agent in a social host, while accounting for the host's explicit movement decisions. We aimed to investigate how temporal mismatches between seasonal resource availability and host life-history events affect host-pathogen coexistence, that is, disease persistence. Seasonal resource fluctuations only increased coexistence probability when in synchrony with the hosts' biological events. However, a temporal mismatch reduced host-pathogen coexistence, but only marginally. In tandem with an increasing temporal mismatch, our model showed a shift in the spatial distribution of infected hosts. It shifted from an even distribution under synchronous conditions toward the formation of disease hotspots, when host life history and resource availability mismatched completely. The spatial restriction of infected hosts to small hotspots in the landscape initially suggested a lower coexistence probability due to the critical loss of susceptible host individuals within those hotspots. However, the surrounding landscape facilitated demographic rescue through habitat-dependent movement. Our work demonstrates that the negative effects of temporal mismatches between host resource availability and host life history on host-pathogen coexistence can be reduced through the formation of temporary disease hotspots and host movement decisions, with implications for disease management under disturbances and global change.
Ecology and evolution
10.1002/ece3.7478
34026043
2045-7758
outputup:dataSource:PubMed:2021
WOS:000634528000001
Kürschner, Tobias (corresponding author), Leibniz Inst Zoo & Wildlife Res, Dept Ecol Dynam, Berlin, Germany., tobias.kuerschner@googlemail.com
Deutsche Forschungsgemeinschaft, German Research Foundation (DFG) [DFG-GRK 2118/1]
Kürschner, Tobias
2024-03-28T07:31:26+00:00
sword
importub
filename=package.tar
115a0d7ed61f73533c16379ff862cce2
false
true
CC-BY - Namensnennung 4.0 International
Tobias Kürschner
Cédric Scherer
Viktoriia Radchuk
Niels Blaum
Stephanie Kramer-Schadt
eng
uncontrolled
classical swine fever
eng
uncontrolled
dynamic landscapes
eng
uncontrolled
global change
eng
uncontrolled
host– pathogen dynamics
eng
uncontrolled
individual‐ based model
eng
uncontrolled
movement ecology
Naturwissenschaften und Mathematik
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
63051
2022
2022
eng
17
7
12
article
Wiley
Hoboken
1
2022-07-11
2022-07-11
--
Large-scale PVA modeling of insects in cultivated grasslands
In many species, dispersal is decisive for survival in a changing climate. Simulation models for population dynamics under climate change thus need to account for this factor. Moreover, large numbers of species inhabiting agricultural landscapes are subject to disturbances induced by human land use. We included dispersal in the HiLEG model that we previously developed to study the interaction between climate change and agricultural land use in single populations. Here, the model was parameterized for the large marsh grasshopper (LMG) in cultivated grasslands of North Germany to analyze (1) the species development and dispersal success depending on the severity of climate change in subregions, (2) the additional effect of grassland cover on dispersal success, and (3) the role of dispersal in compensating for detrimental grassland mowing. Our model simulated population dynamics in 60-year periods (2020-2079) on a fine temporal (daily) and high spatial (250 x 250 m(2)) scale in 107 subregions, altogether encompassing a range of different grassland cover, climate change projections, and mowing schedules. We show that climate change alone would allow the LMG to thrive and expand, while grassland cover played a minor role. Some mowing schedules that were harmful to the LMG nevertheless allowed the species to moderately expand its range. Especially under minor climate change, in many subregions dispersal allowed for mowing early in the year, which is economically beneficial for farmers. More severe climate change could facilitate LMG expansion to uninhabited regions but would require suitable mowing schedules along the path. These insights can be transferred to other species, given that the LMG is considered a representative of grassland communities. For more specific predictions on the dynamics of other species affected by climate change and land use, the publicly available HiLEG model can be easily adapted to the characteristics of their life cycle.
Ecology and evolution
the role of dispersal in mitigating the effects of management schedules under climate change
10.1002/ece3.9063
35845365
2045-7758
outputup:dataSource:WoS:2022
e9063
WOS:000825792900001
Leins, Johannes A. (corresponding author), UFZ Helmholtz Ctr Environm Res, Dept Ecol Modelling, Permoserstr 15, D-04318 Leipzig, Germany., johannes.leins@ufz.de
German Federal Ministry of Education and Research [01LA1803B]
Leins, Johannes A.
2024-03-25T13:34:57+00:00
sword
importub
filename=package.tar
68e238e06bd7bf4280d3eabe98a794f4
false
true
CC-BY - Namensnennung 4.0 International
Johannes A. Leins
Volker Grimm
Martin Drechsler
eng
uncontrolled
bilinear interpolation
eng
uncontrolled
climate change
eng
uncontrolled
dispersal success
eng
uncontrolled
land use
eng
uncontrolled
large marsh grasshopper
eng
uncontrolled
spatially explicit model
Naturwissenschaften und Mathematik
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
63079
2022
2022
eng
16
3
14
article
MDPI
Basel
1
2022-01-22
2022-01-22
--
Estimating the Evaporative Cooling Effect of Irrigation within and above Soybean Canopy
Vegetation with an adequate supply of water might contribute to cooling the land surface around it through the latent heat flux of transpiration. This study investigates the potential estimation of evaporative cooling at plot scale, using soybean as example. Some of the plants' physiological parameters were monitored and sampled at weekly intervals. A physics-based model was then applied to estimate the irrigation-induced cooling effect within and above the canopy during the middle and late season of the soybean growth period. We then examined the results of the temperature changes at a temporal resolution of ten minutes between every two irrigation rounds. During the middle and late season of growth, the cooling effects caused by evapotranspiration within and above the canopy were, on average, 4.4 K and 2.9 K, respectively. We used quality indicators such as R-squared (R-2) and mean absolute error (MAE) to evaluate the performance of the model simulation. The performance of the model in this study was better above the canopy (R-2 = 0.98, MAE = 0.3 K) than below (R-2 = 0.87, MAE = 0.9 K) due to the predefined thermodynamic condition used to estimate evaporative cooling. Moreover, the study revealed that canopy cooling contributes to mitigating heat stress conditions during the middle and late seasons of crop growth.
Water
10.3390/w14030319
2073-4441
outputup:dataSource:WoS:2022
319
WOS:000754655400001
Ghafarian, F (corresponding author), Leibniz Ctr Agr Landscape Res ZALF, Eberswalder Str 84, D-15374 Muncheberg, Germany.; Ghafarian, F (corresponding author), Univ Potsdam, Inst Biochem & Biol, Muhlenberg 3, D-14476 Potsdam, Germany., fatemeh.ghafarian@zalf.de; ralf.wieland@zalf.de; claas.nendel@zalf.de
Federal Ministry of Education and Research (BMBF Forderprogramm; "Agrarsysteme der Zukunft") [031B0729A]
Ghafarian, Fatemeh
2024-03-27T13:18:56+00:00
sword
importub
filename=package.tar
8ae83d955b8a791c8ae495bb171d72ea
false
true
CC-BY - Namensnennung 4.0 International
Fatemeh Ghafarian
Ralf Wieland
Claas Nendel
eng
uncontrolled
canopy cooling effects
eng
uncontrolled
shading cooling
eng
uncontrolled
canopy-air temperature
eng
uncontrolled
energy
eng
uncontrolled
balance
eng
uncontrolled
the Penman-Monteith equation
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
63017
2024
2024
eng
176
doctoralthesis
1
--
--
2024-03-12
Evolution and ontogeny of electric organ discharge in African weakly electric fish genus Campylomormyrus: a genomic and transcriptomic perspective
The African weakly electric fishes (Mormyridae) exhibit a remarkable adaptive radiation possibly due to their species-specific electric organ discharges (EODs). It is produced by a muscle-derived electric organ that is located in the caudal peduncle. Divergence in EODs acts as a pre-zygotic isolation mechanism to drive species radiations. However, the mechanism behind the EOD diversification are only partially understood.
The aim of this study is to explore the genetic basis of EOD diversification from the gene expression level across Campylomormyrus species/hybrids and ontogeny. I firstly produced a high quality genome of the species C. compressirostris as a valuable resource to understand the electric fish evolution.
The next study compared the gene expression pattern between electric organs and skeletal muscles in Campylomormyrus species/hybrids with different types of EOD duration. I identified several candidate genes with an electric organ-specific expression, e.g. KCNA7a, KLF5, KCNJ2, SCN4aa, NDRG3, MEF2. The overall genes expression pattern exhibited a significant association with EOD duration in all analyzed species/hybrids. The expression of several candidate genes, e.g. KCNJ2, KLF5, KCNK6 and KCNQ5, possibly contribute to the regulation of EOD duration in Campylomormyrus due to their increasing or decreasing expression. Several potassium channel genes showed differential expression during ontogeny in species and hybrid with EOD alteration, e.g. KCNJ2.
I next explored allele specific expression of intragenus hybrids by crossing the duration EOD species C. compressirostris with the medium duration EOD species C. tshokwe and the elongated duration EOD species C. rhynchophorus. The hybrids exhibited global expression dominance of the C. compressirostris allele in the adult skeletal muscle and electric organ, as well as in the juvenile electric organ. Only the gene KCNJ2 showed dominant expression of the allele from C. rhynchophorus, and this was increasingly dominant during ontogeny. It hence supported our hypothesis that KCNJ2 is a key gene of regulating EOD duration. Our results help us to understand, from a genetic perspective, how gene expression effect the EOD diversification in the African weakly electric fish.
Die Mormyridae, eine Familie afrikanischer schwach elektrischer Süßwasserfische, zeigen eine außergewöhnliche adaptive Radiation. Eine Erklärung für die Diversifizierung dieser Gruppe stellen die artspezifischen elektrischen Organentladungen (EODs) dar. Diese werden von einem elektrischen Organ muskulären Ursprungs im Ansatz der Schwanzflosse erzeugt. Die verschiedenen EODs könnten als präzygotischer Isolationsmechanismus für die Radiation verantwortlich sein. Dennoch ist der Mechanismus hinter der EOD-Diversifizierung bisher nicht vollständig geklärt.
Ziel dieser Studie ist es, die genetische Grundlage der EOD-Diversifizierung auf der Ebene der Genexpression bei verschiedenen Campylomormyrus-Arten bzw. -Hybriden und während der Ontogenese zu ermitteln. Zunächst wurde erstmals das Genom der Art C. compressirostris in hoher Qualität sequenziert. Dies bildet eine bedeutende Grundlage für das Verständnis der Evolution der elektrischen Fische.
In der zweiten Studie wurden Genexpressionsmuster von elektrischen Organen und Skelettmuskeln bei Campylomormyrus-Arten bzw. -Hybriden mit unterschiedlicher EOD-Dauer verglichen. Dabei konnten mehrere Kandidatengene identifiziert werden, die potentiell Elektroorgan-spezifisch exprimiert sind, i.a. KCNA7a, KLF5, KCNJ2, SCN4aa, NDRG3, MEF2. Bei allen untersuchten Arten/Hybriden wies das Genexpressionsmuster einen signifikanten Zusammenhang mit der EOD-Dauer auf. Die Expression mehrerer Kandidatengene, wie beispielsweise KCNJ2, KLF5, KCNK6 und KCNQ5, trägt möglicherweise zur Regulierung der EOD-Dauer bei Campylomormyrus bei. Bei Arten und Hybriden mit EOD-Unterschieden zeigten Kaliumkanal-Gene wie KCNJ2 eine unterschiedliche Expression während der Ontogenese.
Zudem wurde die Allel-spezifische Expression bei Intragenus-Hybriden unter Verwendung der Arten C. compressirostris, C. tshokwe und C. rhynchophorus, die jeweils eine kurze, intermediäre bzw. lange EOD-Dauer aufweisen, untersucht. Die Hybriden wiesen eine generell dominante Expression der Allele von C. compressirostris in der adulten Skelettmuskulatur und im elektrischen Organ sowie im juvenilen elektrischen Organ auf. Einzig im Gen KCNJ2 dominierte das Allel von C. rhynchophorus, mit zunehmender Dominanz mit fortschreitender Ontogenese. Dies stützt unsere Hypothese einer Beteiligung des KCNJ2-Gens an der Regulation der EOD-Dauer. Unsere Ergebnisse stellen einen wesentlichen Beitrag zum Verständnis des Einflusses der Genexpression auf die EOD-Diversifizierung bei afrikanischen schwach elektrischen Fischen dar.
10.25932/publishup-63017
urn:nbn:de:kobv:517-opus4-630172
online registration
publish
Dissertation, Universität Potsdam, 2024
WG 6730, WH 8730
Keine öffentliche Lizenz: Unter Urheberrechtsschutz
Feng Cheng
eng
uncontrolled
tropical freshwater fish
eng
uncontrolled
weakly electric fish
eng
uncontrolled
genomics
eng
uncontrolled
transcriptomics
deu
uncontrolled
Genomik
deu
uncontrolled
Transkriptomik
deu
uncontrolled
tropische Süßwasserfische
deu
uncontrolled
schwach elektrischer Fisch
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Universität Potsdam
Universität Potsdam
https://publishup.uni-potsdam.de/files/63017/cheng_diss.pdf
56999
2020
2020
eng
13
5
postprint
1
2020-11-20
2020-11-20
--
Role of diversification rates and evolutionary history as a driver of plant naturalization success
Human introductions of species beyond their natural ranges and their subsequent establishment are defining features of global environmental change. However, naturalized plants are not uniformly distributed across phylogenetic lineages, with some families contributing disproportionately more to the global alien species pool than others. Additionally, lineages differ in diversification rates, and high diversification rates have been associated with characteristics that increase species naturalization success. Here, we investigate the role of diversification rates in explaining the naturalization success of angiosperm plant families.
We use five global data sets that include native and alien plant species distribution, horticultural use of plants, and a time-calibrated angiosperm phylogeny. Using phylogenetic generalized linear mixed models, we analysed the effect of diversification rate, different geographical range measures, and horticultural use on the naturalization success of plant families.
We show that a family's naturalization success is positively associated with its evolutionary history, native range size, and economic use. Investigating interactive effects of these predictors shows that native range size and geographic distribution additionally affect naturalization success. High diversification rates and large ranges increase naturalization success, especially of temperate families.
We suggest this may result from lower ecological specialization in temperate families with large ranges, compared with tropical families with smaller ranges.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
urn:nbn:de:kobv:517-opus4-569996
1866-8372
10.25932/publishup-56999
33078849
outputup:dataSource:WoS:2021
WOS:000590686100001
Lenzner, B (corresponding author), Univ Vienna, Dept Bot & Biodivers Res, Rennweg 13, A-1030 Vienna, Austria., bernd.lenzner@univie.ac.at
Austrian Science Foundation FWFAustrian Science Fund (FWF) [I2086-B16,; I3757-B29]; German Research Foundation DFGGerman Research Foundation; (DFG) [264740629, 432253815, FTZ 118]; Czech Science FoundationGrant; Agency of the Czech Republic [19-28807X]; Czech Academy of SciencesCzech; Academy of Sciences [RVO 67985939]; PASPA-DGAPA, UNAMUniversidad; Nacional Autonoma de Mexico; Consejo Nacional de Ciencia y; TecnologiaConsejo Nacional de Ciencia y Tecnologia (CONACyT)
Lenzner, Bernd
2022-12-07T06:37:06+00:00
sword
importub
filename=package.tar
961fa037e7924211f26160b15853fd33
<a href="https://publishup.uni-potsdam.de/56998">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Version of Record
New Phytol, 229: 2998-3008. https://doi.org/10.1111/nph.17014
CC-BY - Namensnennung 4.0 International
Bernd Lenzner
Susana Magallon
Wayne Dawson
Holger Kreft
Christian König
Jan Pergl
Petr Pysek
Patrick Weigelt
Mark van Kleunen
Marten Winter
Stefan Dullinger
Franz Essl
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1363
eng
uncontrolled
alien species
eng
uncontrolled
evolution
eng
uncontrolled
geographic distribution
eng
uncontrolled
invasion success
eng
uncontrolled
plant naturalization
eng
uncontrolled
range size
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Import
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/56999/zmnr1363.pdf
56769
2020
2020
eng
15
4
postprint
1
2020-12-01
2020-12-01
--
Habitat destruction and overexploitation drive widespread declines in all facets of mammalian diversity in the Gran Chaco
Global biodiversity is under high and rising anthropogenic pressure. Yet, how the taxonomic, phylogenetic, and functional facets of biodiversity are affected by different threats over time is unclear. This is particularly true for the two main drivers of the current biodiversity crisis: habitat destruction and overexploitation. We provide the first long-term assessment of multifaceted biodiversity changes caused by these threats for any tropical region. Focussing on larger mammals in South America's 1.1 million km(2) Gran Chaco region, we assessed changes in multiple biodiversity facets between 1985 and 2015, determined which threats drive those changes, and identified remaining key areas for all biodiversity facets. Using habitat and threat maps, we found, first, that between 1985 and 2015 taxonomic (TD), phylogenetic (PD) and functional (FD) diversity all declined drastically across over half of the area assessed. FD declined about 50% faster than TD and PD, and these declines were mainly driven by species loss, rather than species turnover. Second, habitat destruction, hunting, and both threats together contributed similar to 57%, similar to 37%, and similar to 6% to overall facet declines, respectively. However, hunting pressure increased where TD and PD declined most strongly, whereas habitat destruction disproportionally contributed to FD declines. Third, just 23% of the Chaco would have to be protected to safeguard the top 17% of all three facets. Our findings uncover a widespread impoverishment of mammal species richness, evolutionary history, and ecological functions across broad areas of the Chaco due to increasing habitat destruction and hunting. Moreover, our results pinpoint key areas that should be preserved and managed to maintain all facets of mammalian diversity across the Chaco. More generally, our work highlights how long-term changes in biodiversity facets can be assessed and attributed to specific threats, to better understand human impacts on biodiversity and to guide conservation planning to mitigate them.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
urn:nbn:de:kobv:517-opus4-567696
1866-8372
10.25932/publishup-56769
33258510
outputup:dataSource:WoS:2021
WOS:000594391600001
Romero-Munoz, A (corresponding author), Humboldt Univ, Dept Geog, Berlin, Germany., alfredo.romero@geo.hu-berlin.de
Bundesministerium fur Bildung und ForschungFederal Ministry of Education; & Research (BMBF) [031B0034A]; Deutsche ForschungsgemeinschaftGerman; Research Foundation (DFG) [KU 2458/5-1]; Ministerio de Ciencia,; Innovacion y Universidades [IJCI-2017-31419]
Romero-Muñoz, Alfredo
2022-11-21T12:10:31+00:00
sword
importub
filename=package.tar
769ea4f5a7ff08cb24d4c6b4ae6bd0df
<a href="https://publishup.uni-potsdam.de/56768">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Version of Record
Glob Change Biol. 2021; 27: 755–767. https://doi.org/10.1111/gcb.15418
CC-BY - Namensnennung 4.0 International
Alfredo Romero-Munoz
Guillermo Fandos
Ana Benítez-López
Tobias Kuemmerle
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1370
eng
uncontrolled
biodiversity facets
eng
uncontrolled
extinction drivers
eng
uncontrolled
functional diversity
eng
uncontrolled
functional richness
eng
uncontrolled
overhunting
eng
uncontrolled
phylogenetic diversity
eng
uncontrolled
taxonomic
eng
uncontrolled
diversity
eng
uncontrolled
traits
Chemie und zugeordnete Wissenschaften
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Import
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/56769/zmnr1370.pdf
63041
2024
2024
2024
eng
137
doctoralthesis
1
--
--
2024-02-08
Development of a CRISPR/Cas gene editing technique for the coccolithophore Chrysotila carterae
Dissertation, Universität Potsdam, 2024
Katerina Kersting
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Universität Potsdam
Universität Potsdam
63030
2022
2022
eng
E124
E139
16
4
199
article
Univ. of Chicago Press
Chicago
1
2022-02-14
2022-02-14
--
Fluctuations in density-dependent selection drive the evolution of a pace-of-life syndrome within and between populations
The pace-of-life syndrome (POLS) hypothesis posits that suites of traits are correlated along a slow-fast continuum owing to life history trade-offs. Despite widespread adoption, environmental conditions driving the emergence of POLS remain unclear. A recently proposed conceptual framework of POLS suggests that a slow-fast continuum should align to fluctuations in density-dependent selection. We tested three key predictions made by this framework with an ecoevolutionary agent-based population model. Selection acted on responsiveness (behavioral trait) to interpatch resource differences and the reproductive investment threshold (life history trait). Across environments with density fluctuations of different magnitudes, we observed the emergence of a common axis of trait covariation between and within populations (i.e., the evolution of a POLS). Slow-type (fast-type) populations with high (low) responsiveness and low (high) reproductive investment threshold were selected at high (low) population densities and less (more) intense and frequent density fluctuations. In support of the predictions, fast-type populations contained a higher degree of variation in traits and were associated with higher intrinsic reproductive rate (r(0)) and higher sensitivity to intraspecific competition (gamma), pointing to a universal trade-off. While our findings support that POLS aligns with density-dependent selection, we discuss possible mechanisms that may lead to alternative evolutionary pathways.
The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences
10.1086/718473
35324382
0003-0147
1537-5323
outputup:dataSource:WoS:2022
WOS:000756956600002
Milles, Alexander (corresponding author), Univ Potsdam, Plant Ecol & Nat Conservat, Muhlenberg 3, D-14476 Potsdam, Germany.; Milles, A (corresponding author), UFZ Helmholtz Ctr Environm Res, Dept Ecol Modelling, Permoserstr 15, D-04318 Leipzig, Germany., alexander.milles@uni-potsdam.de
German Research Foundation (DFG) [DFG-GRK 2118/1]; German Science; Foundation [DA 1377/4-1]
Milles, Alexander
2024-03-21T09:19:57+00:00
sword
importub
filename=package.tar
179027e1274a84efd8f9b77ad455130b
CC-BY-NC - Namensnennung, nicht kommerziell 4.0 International
Alexander Benedikt Milles
Melanie Dammhahn
Florian Jeltsch
Ulrike Schlägel
Volker Grimm
eng
uncontrolled
pace-of-life syndrome
eng
uncontrolled
density dependence
eng
uncontrolled
life history
eng
uncontrolled
trait
eng
uncontrolled
variation
eng
uncontrolled
model
eng
uncontrolled
personality
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
56952
2020
2020
eng
17
1
postprint
1
2020-11-26
2020-11-26
--
Manipulation of cytosine methylation does not remove latitudinal clines in two invasive goldenrod species in Central Europe
Invasive species frequently differentiate phenotypically in novel environments within a few generations, often even with limited genetic variation. For the invasive plants Solidago canadensis and S. gigantea, we tested whether such differentiation might have occurred through heritable epigenetic changes in cytosine methylation. In a 2-year common-garden experiment, we grew plants from seeds collected along a latitudinal gradient in their non-native Central European range to test for trait differentiation and whether differentiation disappeared when seeds were treated with the demethylation agent zebularine. Microsatellite markers revealed no population structure along the latitudinal gradient in S. canadensis, but three genetic clusters in S. gigantea. Solidago canadensis showed latitudinal clines in flowering phenology and growth. In S. gigantea, the number of clonal offspring decreased with latitude. Although zebularine had a significant effect on early growth, probably through effects on cytosine methylation, latitudinal clines remained (or even got stronger) in plants raised from seeds treated with zebularine. Thus, our experiment provides no evidence that epigenetic mechanisms by selective cytosine methylation contribute to the observed phenotypic differentiation in invasive goldenrods in Central Europe.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-56952
urn:nbn:de:kobv:517-opus4-569528
1866-8372
33150604
outputup:dataSource:WoS:2021
WOS:000592211700001
Eckert, S (corresponding author), Univ Potsdam, Inst Biochem & Biol, Biodivers Res Systemat Bot, Potsdam, Germany., silvia.eckert@uni-potsdam.de
Deutsche ForschungsgemeinschaftGerman Research Foundation (DFG) [SPP1819; (JO 777/8-1), KL1866/10-1]
Eckert, Silvia
2022-12-02T10:23:15+00:00
sword
importub
filename=package.tar
2c6cbf27cfa1376120c69dd66d75fad5
<a href="https://publishup.uni-potsdam.de/56951">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Mol Ecol. 2021; 30: 222–236. https://doi.org/10.1111/mec.15722
Version of Record
CC-BY-NC - Namensnennung, nicht kommerziell 4.0 International
Silvia Eckert
Jasmin Herden
Marc Stift
Jasmin Radha Joshi
Mark van Kleunen
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1378
eng
uncontrolled
common‐garden experiment
eng
uncontrolled
epigenetic variation
eng
uncontrolled
microsatellites
eng
uncontrolled
Solidago canadensis
eng
uncontrolled
Solidago gigantea
eng
uncontrolled
zebularine
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Import
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/56952/zmnr1378.pdf
56956
2020
2020
eng
19
4
postprint
1
2020-11-25
2020-11-25
--
Regulation of shoot branching in arabidopsis by trehalose 6-phosphate
Trehalose 6-phosphate (Tre6P) is a sucrose signalling metabolite that has been implicated in regulation of shoot branching, but its precise role is not understood.
We expressed tagged forms of TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) to determine where Tre6P is synthesized in arabidopsis (Arabidopsis thaliana), and investigated the impact of localized changes in Tre6P levels, in axillary buds or vascular tissues, on shoot branching in wild-type and branching mutant backgrounds.
TPS1 is expressed in axillary buds and the subtending vasculature, as well as in the leaf and stem vasculature. Expression of a heterologous Tre6P phosphatase (TPP) to lower Tre6P in axillary buds strongly delayed bud outgrowth in long days and inhibited branching in short days. TPP expression in the vasculature also delayed lateral bud outgrowth and decreased branching. Increased Tre6P in the vasculature enhanced branching and was accompanied by higher expression of FLOWERING LOCUS T (FT) and upregulation of sucrose transporters. Increased vascular Tre6P levels enhanced branching in branched1 but not in ft mutant backgrounds.
These results provide direct genetic evidence of a local role for Tre6P in regulation of axillary bud outgrowth within the buds themselves, and also connect Tre6P with systemic regulation of shoot branching via FT.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-56956
urn:nbn:de:kobv:517-opus4-569564
1866-8372
33068448
outputup:dataSource:WoS:2021
WOS:000592039700001
Fichtner, F; Lunn, JE (corresponding author), Max Planck Inst Mol Plant Physiol, D-14476 Potsdam, Germany.; Fichtner, F (corresponding author), Univ Queensland, Sch Biol Sci, St Lucia, Qld 4072, Australia., f.fichtner@uq.edu.au; lunn@mpimp-golm.mpg.de
International Max Planck Research School - Primary Metabolism and Plant; Growth; Australian Research CouncilAustralian Research Council; [DP150102086, FL180100139]; Max Planck SocietyMax Planck; SocietyFoundation CELLEX; Deutsche Forschungsgemeinschaft (DFG; within; the Collaborative Research Centre 973)
Fichtner, Franziska
2022-12-05T07:09:06+00:00
sword
importub
filename=package.tar
f5eb9bbae1cced9f7f7c99ab43f20acb
<a href="https://publishup.uni-potsdam.de/56955">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
New Phytol, 229: 2135-2151. https://doi.org/10.1111/nph.17006
Version of Record
CC-BY-NC-ND - Namensnennung, nicht kommerziell, keine Bearbeitungen 4.0 International
Franziska Fichtner
Francois F. Barbier
Maria Grazia Annunziata
Regina Feil
Justyna Jadwiga Olas
Bernd Müller-Röber
Mark Stitt
Christine A. Beveridge
John Edward Lunn
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1383
eng
uncontrolled
Arabidopsis thaliana (arabidopsis)
eng
uncontrolled
axillary bud
eng
uncontrolled
branching
eng
uncontrolled
sucrose
eng
uncontrolled
sugar signalling
eng
uncontrolled
trehalose 6‐ phosphate (Tre6P)
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Import
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/56956/zmnr1383.pdf
57351
2020
2020
eng
16
1
postprint
1
2020-11-13
2020-11-13
--
Grasses cope with high-contrast ecosystem conditions in the large outflow of the Banhine wetlands, Mozambique
Ecosystems with highly pulsed water supply must be better understood as climate change may increase frequency and severity of intense storms, droughts and floods. Here we collected data over 3 years (2016-2018) in the episodic wetland outflow channel (Aluize), Banhine National Park, in which the system state changed from dry to wet to dry. Field sampling included vegetation records, small-scale vegetation zoning, the seed bank and water and soil quality. The same main plant species were found in both dry and wet conditions across the riverbed of the outflow channel. We found only very few diaspores of plants in the soil after prolonged drought. In the subsequent flooded state, we examined very dense vegetation on the water surface, which was dominated by the gramineous species Paspalidium obtusifolium. This species formed a compact floating mat that was rooted to the riverbed. The Cyperaceae Bolboschoenus glaucus showed high clonal growth in the form of root tubers, which likely serve as important food reservoir during drought. Soil and water analyses do not indicate a limitation by nutrients. We outline how resident people may change the plant community structure with an increasing practice of setting fire to the meadows in the dried-up riverbed to facilitate plant regrowth as food for their livestock.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-57351
urn:nbn:de:kobv:517-opus4-573515
1866-8372
outputup:dataSource:WoS:2021
WOS:000588831600001
Zaplata, MK (corresponding author), Brandenburg Univ Technol Cottbus Senftenberg, Cottbus, Germany.; Sperfeld, E (corresponding author), Ernst Moritz Arndt Univ Greifswald, Zool Inst & Museum, Anim Ecol, Loitzer Str 26, D-17489 Greifswald, Germany., zaplata@wzw.tum.de; erik.sperfeld@uni-greifswald.de
Projekt DEAL
Zaplata, Markus Klemens
2023-01-06T08:24:22+00:00
sword
importub
filename=package.tar
3526ccefa91a0babcba9a228f21be5b5
<a href="https://publishup.uni-potsdam.de/57350">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Afr J Ecol. 2021; 59: 190–203. https://doi.org/10.1111/aje.12820
Version of Record
CC-BY-NC - Namensnennung, nicht kommerziell 4.0 International
Markus Klemens Zaplata
Abel Nhabanga
Marc Stalmans
Thomas Volpers
Michael Burkart
Erik Sperfeld
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1386
eng
uncontrolled
Aluize
eng
uncontrolled
biological soil crusts
eng
uncontrolled
Changane
eng
uncontrolled
droughts
eng
uncontrolled
floating mat
eng
uncontrolled
flooded grasslands
eng
uncontrolled
multi‐ year flooding cycle
eng
uncontrolled
plant clonality
eng
uncontrolled
seed bank
eng
uncontrolled
temporary wetland
Biowissenschaften; Biologie
Pflanzen (Botanik)
open_access
Institut für Biochemie und Biologie
Referiert
Import
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/57351/zmnr1386.pdf
62856
2024
2024
eng
xiv, 168
doctoralthesis
1
--
--
2024-02-26
A study on Coronin-A and Aip1 function in motility of Dictyostelium discoideum and on Aip1 interchangeability between Dictyostelium discoideum and Arabidopsis thaliana
Studie über die Funktion von Coronin-A und Aip1 bei der Motilität von Dictyostelium discoideum und zur Aip1-Austauschbarkeit zwischen Dictyostelium discoideum und Arabidopsis thaliana
Actin is one of the most highly conserved proteins in eukaryotes and distinct actin-related proteins with filament-forming properties are even found in prokaryotes. Due to these commonalities, actin-modulating proteins of many species share similar structural properties and proposed functions. The polymerization and depolymerization of actin are critical processes for a cell as they can contribute to shape changes to adapt to its environment and to move and distribute nutrients and cellular components within the cell. However, to what extent functions of actin-binding proteins are conserved between distantly related species, has only been addressed in a few cases. In this work, functions of Coronin-A (CorA) and Actin-interacting protein 1 (Aip1), two proteins involved in actin dynamics, were characterized. In addition, the interchangeability and function of Aip1 were investigated in two phylogenetically distant model organisms. The flowering plant Arabidopsis thaliana (encoding two homologs, AIP1-1 and AIP1-2) and in the amoeba Dictyostelium discoideum (encoding one homolog, DdAip1) were chosen because the functions of their actin cytoskeletons may differ in many aspects. Functional analyses between species were conducted for AIP1 homologs as flowering plants do not harbor a CorA gene.
In the first part of the study, the effect of four different mutation methods on the function of Coronin-A protein and the resulting phenotype in D. discoideum was revealed in two genetic knockouts, one RNAi knockdown and a sudden loss-of-function mutant created by chemical-induced dislocation (CID). The advantages and disadvantages of the different mutation methods on the motility, appearance and development of the amoebae were investigated, and the results showed that not all observed properties were affected with the same intensity. Remarkably, a new combination of Selection-Linked Integration and CID could be established.
In the second and third parts of the thesis, the exchange of Aip1 between plant and amoeba was carried out. For A. thaliana, the two homologs (AIP1-1 and AIP1-2) were analyzed for functionality as well as in D. discoideum. In the Aip1-deficient amoeba, rescue with AIP1-1 was more effective than with AIP1-2. The main results in the plant showed that in the aip1-2 mutant background, reintroduced AIP1-2 displayed the most efficient rescue and A. thaliana AIP1-1 rescued better than DdAip1. The choice of the tagging site was important for the function of Aip1 as steric hindrance is a problem. The DdAip1 was less effective when tagged at the C-terminus, while the plant AIP1s showed mixed results depending on the tag position. In conclusion, the foreign proteins partially rescued phenotypes of mutant plants and mutant amoebae, despite the organisms only being very distantly related in evolutionary terms.
Actin ist eines der am stärksten konservierten Proteine in Eukaryoten und sogar Prokaryoten weisen Aktin-ähnliche Proteine mit filamentbildenden Eigenschaften auf. Aufgrund dieser Gemeinsamkeiten teilen Aktin-modulierte Proteine vieler Arten ähnliche strukturelle Eigenschaften und vermutlich auch Funktionen. Die Polymerisierung und Depolymerisation von Aktin sind kritische Prozesse für eine Zelle, da sie zu Zellformänderungen beitragen können, um sich an die Umgebung anzupassen und Nährstoffe sowie zelluläre Komponenten innerhalb der Zelle zu bewegen und zu verteilen. Inwieweit die Funktionen von Aktin-bindenden Proteinen zwischen entfernt verwandten Arten funktionell konserviert sind, wurde jedoch nur in wenigen Fällen untersucht. In dieser Arbeit wurden Funktionen von Coronin-A (CorA) und Actin-interagierendem Protein 1 (AIP1), zweier an der Aktindynamik beteiligter Proteine, charakterisiert. Darüber hinaus wurde die Austauschbarkeit und Funktion von AIP1 in zwei phylogenetisch entfernten Modellorganismen untersucht. Die Blütenpflanze Arabidopsis thaliana (kodiert für zwei Homologe: AIP1-1 und AIP1-2) und die Amöbe Dictyostelium discoideum (kodiert für ein Homolog: DdAip1) wurden ausgewählt, weil die Funktionen ihrer Aktin-Zytoskelette in mehreren Aspekten verschieden sein könnten. Funktionelle Analysen zwischen Arten wurden für AIP1-Homologe durchgeführt, da Blütenpflanzen kein CorA Gen tragen.
Im ersten Teil der Arbeit wurde die Wirkung von vier verschiedenen Mutationsmethoden auf die Funktion des CorA-Proteins und des resultierenden Phänotyps in D. discoideum in zwei genetischen Knockouts, einem RNAi Knockdown und einem durch chemisch induzierte Delokalisierung (CID) erzeugten Mutanten geprüft. Die Vor- und Nachteile der Methoden zur Motilität, des Aussehens und der Entwicklung der Amöben wurden untersucht. Die Ergebnisse zeigten, dass nicht alle beobachteten Eigenschaften mit der gleichen Intensität beeinflusst wurden. Hierbei wurde eine neue Methodenkombination aus selektionsgebundener Integration und CID etabliert.
Im zweiten und im dritten Teil der Arbeit wurde der Austausch von AIP1 zwischen Pflanze und Amöben durchgeführt. Die zwei A. thaliana-Homologe AIP1-1 und AIP1-2 wurden auf Funktionalität in D. discoideum geprüft. In Aip1-defizienten Amöben war die Rettung mit AIP1-1 effektiver als bei AIP1-2. Die Hauptergebnisse der Arbeit wiesen darauf hin, dass AIP1-2 im aip1.2-1 act7 Mutantenhintergrund die effizienteste Rettung zeigte, während A. thaliana AIP1-1 effizienter rettete als DdAip1. Die Auswahl der Tagging-Site war für die AIP1-Funktion bedeutend, da sterische Hinderung eine Rolle spielen könnte. DdAip1 war weniger effektiv, wenn es am C-Terminus fusioniert war, während die Proteinfusionen der A. thaliana AIP1s je nach Position der „tags“ unterschiedliche Ergebnisse zeigten. Zusammenfassend retteten die fremden Proteine teilweise Phänotypen von mutierten Pflanzen und mutierten Amöben, obwohl die Organismen evolutionär weit entfernt verwandt sind.
10.25932/publishup-62856
urn:nbn:de:kobv:517-opus4-628569
online registration
publish
Dissertation, Universität Potsdam, 2024
WE 2920, WG 3450
CC-BY-NC-ND - Namensnennung, nicht kommerziell, keine Bearbeitungen 4.0 International
Maike Stange
eng
uncontrolled
actin
eng
uncontrolled
cell motility
eng
uncontrolled
plant growth
eng
uncontrolled
selection-linked integration
eng
uncontrolled
chemically induced dislocation
eng
uncontrolled
interspecies interchange
deu
uncontrolled
Aktin
deu
uncontrolled
Zellmotilität
deu
uncontrolled
Pflanzenwachstum
deu
uncontrolled
Selection-Linked Integration
deu
uncontrolled
chemisch-induzierte Dislokation
deu
uncontrolled
Austausch zwischen zwei Spezies
Biowissenschaften; Biologie
Cell biology
open_access
Institut für Physik und Astronomie
Institut für Biochemie und Biologie
Universität Potsdam
Universität Potsdam
https://publishup.uni-potsdam.de/files/62856/stange_diss.pdf
51395
2020
2020
eng
14
6
postprint
1
2020-03-03
2020-03-03
--
The shape of a defense-growth trade-off governs seasonal trait dynamics in natural phytoplankton
Theory predicts that trade-offs, quantifying costs of functional trait adjustments, crucially affect community trait adaptation to altered environmental conditions, but empirical verification is scarce. We evaluated trait dynamics (antipredator defense, maximum growth rate, and phosphate affinity) of a lake phytoplankton community in a seasonally changing environment, using literature trait data and 21 years of species-resolved high-frequency biomass measurements. The trait data indicated a concave defense-growth trade-off, promoting fast-growing species with intermediate defense. With seasonally increasing grazing pressure, the community shifted toward higher defense levels at the cost of lower growth rates along the trade-off curve, while phosphate affinity explained some deviations from it. We discuss how low fitness differences of species, inferred from model simulations, in concert with stabilizing mechanisms, e.g., arising from further trait dimensions, may lead to the observed phytoplankton diversity. In conclusion, quantifying trade-offs is key for predictions of community trait adaptation and biodiversity under environmental change.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-51395
urn:nbn:de:kobv:517-opus4-513956
1866-8372
32127656
online registration
publish
<a href="http://publishup.uni-potsdam.de/57563">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
ISME J 14, 1451–1462 (2020). https://doi.org/10.1038/s41396-020-0619-1
Version of Record
false
true
CC-BY - Namensnennung 4.0 International
Elias Ehrlich
Nadja Jeanette Kath
Ursula Gaedke
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1390
eng
uncontrolled
functional traits
eng
uncontrolled
community ecology
eng
uncontrolled
evolution
eng
uncontrolled
lake
eng
uncontrolled
mechanisms
eng
uncontrolled
diversity
eng
uncontrolled
plankton
eng
uncontrolled
fitness
eng
uncontrolled
maintenance
eng
uncontrolled
coexistence
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51395/zmnr1390.pdf
51582
2020
2020
eng
16
1
postprint
1
2020-01-16
2020-01-16
--
Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran
Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-51582
urn:nbn:de:kobv:517-opus4-515820
1866-8372
online registration
publish
<a href="http://publishup.uni-potsdam.de/61085">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Aquat Ecol 54, 323–336 (2020). https://doi.org/10.1007/s10452-019-09745-w
Version of Record
false
true
CC-BY - Namensnennung 4.0 International
Hossein Masigol
Seyed Akbar Khodaparast
Reza Mostowfizadeh-Ghalamfarsa
Keilor Rojas-Jimenez
Jason Nicholas Woodhouse
Darshan Neubauer
Hans-Peter Grossart
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1395
eng
uncontrolled
Achlya
eng
uncontrolled
Saprolegnia
eng
uncontrolled
aquatic ecosystems
eng
uncontrolled
carbon cycling
eng
uncontrolled
polymer degradation
eng
uncontrolled
Saprolegniaceae
eng
uncontrolled
Achlyaceae
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51582/zmnr1395.pdf
61085
2020
2020
eng
323
336
14
1
54
article
Springer Science
Dordrecht
1
2020-01-16
2020-01-16
--
Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran
Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems.
Aquatic Ecology
10.1007/s10452-019-09745-w
1573-5125
1386-2588
Hans-Peter F. Grossart
1411979-1
<a href="https://doi.org/10.25932/publishup-51582">Zweitveröffentlichung in der Schriftenreihe Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1395</a>
CC-BY - Namensnennung 4.0 International
Hossein Masigol
Seyed Akbar Khodaparast
Reza Mostowfizadeh-Ghalamfarsa
Keilor Rojas-Jimenez
Jason Nicholas Woodhouse
Darshan Neubauer
Hans-Peter Grossart
eng
uncontrolled
Achlya
eng
uncontrolled
Saprolegnia
eng
uncontrolled
aquatic ecosystems
eng
uncontrolled
carbon cycling
eng
uncontrolled
polymer degradation
eng
uncontrolled
Saprolegniaceae
eng
uncontrolled
Achlyaceae
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Hybrid Open-Access
62979
2022
2022
eng
1309
1321
13
12
43
article
Wiley-Blackwell
Weinheim
1
2022-01-01
2022-03-21
--
AC electrokinetic immobilization of influenza virus
The use of alternating current (AC) electrokinetic forces, like dielectrophoresis and AC electroosmosis, as a simple and fast method to immobilize sub-micrometer objects onto nanoelectrode arrays is presented. Due to its medical relevance, the influenza virus is chosen as a model organism. One of the outstanding features is that the immobilization of viral material to the electrodes can be achieved permanently, allowing subsequent handling independently from the electrical setup. Thus, by using merely electric fields, we demonstrate that the need of prior chemical surface modification could become obsolete. The accumulation of viral material over time is observed by fluorescence microscopy. The influences of side effects like electrothermal fluid flow, causing a fluid motion above the electrodes and causing an intensity gradient within the electrode array, are discussed. Due to the improved resolution by combining fluorescence microscopy with deconvolution, it is shown that the viral material is mainly drawn to the electrode edge and to a lesser extent to the electrode surface. Finally, areas of application for this functionalization technique are presented.
Electrophoresis : microfluids & proteomics
10.1002/elps.202100324
35307846
0173-0835
1522-2683
outputup:dataSource:WoS:2022
WOS:000789570000001
Hölzel, R (corresponding author), Fraunhofer Inst Cell Therapy & Immunol, Branch Bioanalyt & Bioproc IZI BB, D-14476 Potsdam, Germany., sandra.stanke@izi-bb.fraunhofer.de
Deutsche Forschungsgemeinschaft [SPP1857, HO1298/4-1]; European Regional; Development Fund; Ministerium fur Wissenschaft, Forschung und Kultur; [85004117]; German Academic Scholarship Foundation
Hölzel, Ralph
2024-03-15T09:32:23+00:00
sword
importub
filename=package.tar
2bf907e287860415f4f9945443f95a2b
false
true
CC-BY-NC - Namensnennung, nicht kommerziell 4.0 International
Sandra Stanke
Christian Wenger
Frank Fabian Bier
Ralph Hölzel
eng
uncontrolled
AC electrokinetics
eng
uncontrolled
AC electroosmosis
eng
uncontrolled
dielectrophoresis
eng
uncontrolled
influenza virus
eng
uncontrolled
nanoelectrodes
Chemie und zugeordnete Wissenschaften
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
62965
2022
2022
eng
11
9
article
Oxford Univ. Press
Cary
1
2022-03-23
2022-03-23
--
Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits
Selection of high-performance lines with respect to traits of interest is a key step in plant breeding. Genomic prediction allows to determine the genomic estimated breeding values of unseen lines for trait of interest using genetic markers, e.g. single-nucleotide polymorphisms (SNPs), and machine learning approaches, which can therefore shorten breeding cycles, referring to genomic selection (GS). Here, we applied GS approaches in two populations of Solanaceous crops, i.e. tomato and pepper, to predict morphometric and colorimetric traits. The traits were measured by using scoring-based conventional descriptors (CDs) as well as by Tomato Analyzer (TA) tool using the longitudinally and latitudinally cut fruit images. The GS performance was assessed in cross-validations of classification-based and regression-based machine learning models for CD and TA traits, respectively. The results showed the usage of TA traits and tag SNPs provide a powerful combination to predict morphology and color-related traits of Solanaceous fruits. The highest predictability of 0.89 was achieved for fruit width in pepper, with an average predictability of 0.69 over all traits. The multi-trait GS models are of slightly better predictability than single-trait models for some colorimetric traits in pepper. While model validation performs poorly on wild tomato accessions, the usage as many as one accession per wild species in the training set can increase the transferability of models to unseen populations for some traits (e.g. fruit shape for which predictability in unseen scenario increased from zero to 0.6). Overall, GS approaches can assist the selection of high-performance Solanaceous fruits in crop breeding.
Horticulture research
10.1093/hr/uhac072
35669711
2052-7276
outputup:dataSource:WoS:2022
uhac072
WOS:000828691700068
Nikoloski, Z (corresponding author), Ctr Plant Syst Biol & Biotechnol, Plovdiv 4000, Bulgaria.; Nikoloski, Z (corresponding author), Max Planck Inst Mol Plant Physiol, Syst Biol & Math Modeling, D-14476 Potsdam, Germany.; Nikoloski, Z (corresponding author), Univ Potsdam, Inst Biochem & Biol, Bioinformat, D-14476 Potsdam, Germany., nikoloski@mpimp-golm.mpg.de
European Union [739582, 664620]; European Regional Development Fund; through the Bulgarian "Science and Education for Smart Growth"; Operational Programme [BG05M2OP001-1.003-001-C01]
Nikoloski, Zoran
2024-03-14T12:40:31+00:00
sword
importub
filename=package.tar
d42c0400da5dea534e199ffcab427fb3
false
true
CC-BY - Namensnennung 4.0 International
Hao Tong
Amol N. Nankar
Jintao Liu
Velichka Todorova
Daniela Ganeva
Stanislava Grozeva
Ivanka Tringovska
Gancho Pasev
Vesela Radeva-Ivanova
Tsanko Gechev
Dimitrina Kostova
Zoran Nikoloski
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
51366
2020
2020
eng
20
1
postprint
1
2020-03-19
2020-03-19
--
Specific functions for mediator complex subunits from different modules in the transcriptional response of arabidopsis thaliana to abiotic stress
Adverse environmental conditions are detrimental to plant growth and development. Acclimation to abiotic stress conditions involves activation of signaling pathways which often results in changes in gene expression via networks of transcription factors (TFs). Mediator is a highly conserved co-regulator complex and an essential component of the transcriptional machinery in eukaryotes. Some Mediator subunits have been implicated in stress-responsive signaling pathways; however, much remains unknown regarding the role of plant Mediator in abiotic stress responses. Here, we use RNA-seq to analyze the transcriptional response of Arabidopsis thaliana to heat, cold and salt stress conditions. We identify a set of common abiotic stress regulons and describe the sequential and combinatorial nature of TFs involved in their transcriptional regulation. Furthermore, we identify stress-specific roles for the Mediator subunits MED9, MED16, MED18 and CDK8, and putative TFs connecting them to different stress signaling pathways. Our data also indicate different modes of action for subunits or modules of Mediator at the same gene loci, including a co-repressor function for MED16 prior to stress. These results illuminate a poorly understood but important player in the transcriptional response of plants to abiotic stress and identify target genes and mechanisms as a prelude to further biochemical characterization.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-51366
urn:nbn:de:kobv:517-opus4-513666
1866-8372
32193425
online registration
publish
<a href="http://publishup.uni-potsdam.de/58427">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Sci Rep 10, 5073 (2020). https://doi.org/10.1038/s41598-020-61758-w
Version of Record
false
true
CC-BY - Namensnennung 4.0 International
Tim Crawford
Fazeelat Karamat
Nóra Lehotai
Matilda Rentoft
Jeanette Blomberg
Åsa Strand
Stefan Björklund
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1399
eng
uncontrolled
regulate gene expression
eng
uncontrolled
signal transduction
eng
uncontrolled
circadian clock
eng
uncontrolled
plant Mediator
eng
uncontrolled
salicylic-acid
eng
uncontrolled
activation
eng
uncontrolled
jasmonate
eng
uncontrolled
network
eng
uncontrolled
defense
eng
uncontrolled
MED16
Naturwissenschaften und Mathematik
Biowissenschaften; Biologie
Technik, Technologie
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51366/zmnr1399.pdf
51569
2020
2020
eng
17
1
postprint
1
2020-03-06
2020-03-06
--
mRNA transfection-induced activation of primary human monocytes and macrophages
Monocytes and macrophages are key players in maintaining immune homeostasis. Identifying strategies to manipulate their functions via gene delivery is thus of great interest for immunological research and biomedical applications. We set out to establish conditions for mRNA transfection in hard-to-transfect primary human monocytes and monocyte-derived macrophages due to the great potential of gene expression from in vitro transcribed mRNA for modulating cell phenotypes. mRNA doses, nucleotide modifications, and different carriers were systematically explored in order to optimize high mRNA transfer rates while minimizing cell stress and immune activation. We selected three commercially available mRNA transfection reagents including liposome and polymer-based formulations, covering different application spectra. Our results demonstrate that liposomal reagents can particularly combine high gene transfer rates with only moderate immune cell activation. For the latter, use of specific nucleotide modifications proved essential. In addition to improving efficacy of gene transfer, our findings address discrete aspects of innate immune activation using cytokine and surface marker expression, as well as cell viability as key readouts to judge overall transfection efficiency. The impact of this study goes beyond optimizing transfection conditions for immune cells, by providing a framework for assessing new gene carrier systems for monocyte and macrophage, tailored to specific applications.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
Dependence on carrier system and nucleotide modifcation
10.25932/publishup-51569
urn:nbn:de:kobv:517-opus4-515694
1866-8372
online registration
publish
<a href="http://publishup.uni-potsdam.de/61351">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Sci Rep 10, 4181 (2020). https://doi.org/10.1038/s41598-020-60506-4
Version of Record
false
true
CC-BY - Namensnennung 4.0 International
Hanieh Moradian
Toralf Roch
Andreas Lendlein
Manfred Gossen
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1403
eng
uncontrolled
sirna transfection
eng
uncontrolled
mediated delivery
eng
uncontrolled
gene delivery
eng
uncontrolled
efficient
eng
uncontrolled
immunogenicity
eng
uncontrolled
lipoplexes
eng
uncontrolled
cells
eng
uncontrolled
therapeutics
eng
uncontrolled
polarization
eng
uncontrolled
pathways
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51569/zmnr1403.pdf
61351
2020
2020
eng
1
15
15
1
10
article
Springer Nature
London
1
2020-03-06
2020-03-06
--
mRNA transfection-induced activation of primary human monocytes and macrophages
Monocytes and macrophages are key players in maintaining immune homeostasis. Identifying strategies to manipulate their functions via gene delivery is thus of great interest for immunological research and biomedical applications. We set out to establish conditions for mRNA transfection in hard-to-transfect primary human monocytes and monocyte-derived macrophages due to the great potential of gene expression from in vitro transcribed mRNA for modulating cell phenotypes. mRNA doses, nucleotide modifications, and different carriers were systematically explored in order to optimize high mRNA transfer rates while minimizing cell stress and immune activation. We selected three commercially available mRNA transfection reagents including liposome and polymer-based formulations, covering different application spectra. Our results demonstrate that liposomal reagents can particularly combine high gene transfer rates with only moderate immune cell activation. For the latter, use of specific nucleotide modifications proved essential. In addition to improving efficacy of gene transfer, our findings address discrete aspects of innate immune activation using cytokine and surface marker expression, as well as cell viability as key readouts to judge overall transfection efficiency. The impact of this study goes beyond optimizing transfection conditions for immune cells, by providing a framework for assessing new gene carrier systems for monocyte and macrophage, tailored to specific applications.
Scientific reports
Dependence on carrier system and nucleotide modifcation
10.1038/s41598-020-60506-4
2045-2322
4181
Manfred Gossen
2615211-3
<a href="https://doi.org/10.25932/publishup-51569">Zweitveröffentlichung in der Schriftenreihe Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1403</a>
CC-BY - Namensnennung 4.0 International
Hanieh Moradian
Toralf Roch
Andreas Lendlein
Manfred Gossen
eng
uncontrolled
sirna transfection
eng
uncontrolled
mediated delivery
eng
uncontrolled
gene delivery
eng
uncontrolled
efficient
eng
uncontrolled
immunogenicity
eng
uncontrolled
lipoplexes
eng
uncontrolled
cells
eng
uncontrolled
therapeutics
eng
uncontrolled
polarization
eng
uncontrolled
pathways
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Gold Open-Access
DOAJ gelistet
51666
2020
2020
eng
13
17
postprint
1
2020-02-20
2020-02-20
--
Chromatin regulation of somatic abiotic stress memory
In nature, plants are often subjected to periods of recurrent environmental stress that can strongly affect their development and productivity. To cope with these conditions, plants can remember a previous stress, which allows them to respond more efficiently to a subsequent stress, a phenomenon known as priming. This ability can be maintained at the somatic level for a few days or weeks after the stress is perceived, suggesting that plants can store information of a past stress during this recovery phase. While the immediate responses to a single stress event have been extensively studied, knowledge on priming effects and how stress memory is stored is still scarce. At the molecular level, memory of a past condition often involves changes in chromatin structure and organization, which may be maintained independently from transcription. In this review, we will summarize the most recent developments in the field and discuss how different levels of chromatin regulation contribute to priming and plant abiotic stress memory.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-51666
urn:nbn:de:kobv:517-opus4-516668
1866-8372
32076719
online registration
publish
<a href="http://publishup.uni-potsdam.de/56820">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Journal of Experimental Botany, Volume 71, Issue 17, 17 August 2020, Pages 5269–5279, https://doi.org/10.1093/jxb/eraa098
Version of Record
false
true
CC-BY - Namensnennung 4.0 International
Isabel Bäurle
Inês Trindade
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1408
eng
uncontrolled
abiotic stress
eng
uncontrolled
chromatin regulation
eng
uncontrolled
heat stress memory
eng
uncontrolled
histone modifications, priming
eng
uncontrolled
transcriptional memory
eng
uncontrolled
vernalization
Pflanzen (Botanik)
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51666/zmnr1408.pdf
51604
2020
2020
eng
12
1
postprint
1
2020-01-17
2020-01-17
--
A new lineage of segmented RNA viruses infecting animals
Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-51604
urn:nbn:de:kobv:517-opus4-516040
1866-8372
online registration
publish
<a href="http://publishup.uni-potsdam.de/61416">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Virus Evolution, Volume 6, Issue 1, January 2020, vez061, https://doi.org/10.1093/ve/vez061
Version of Record
false
true
CC-BY - Namensnennung 4.0 International
Darren J. Obbard
Mang Shi
Katherine E. Roberts
Ben Longdon
Alice B. Dennis
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1411
eng
uncontrolled
metagenome
eng
uncontrolled
RNA virus
eng
uncontrolled
dark virus
eng
uncontrolled
arthropod
eng
uncontrolled
RNA interference
Biowissenschaften; Biologie
Tiere (Zoologie)
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51604/zmnr1411.pdf
61416
2020
2020
eng
1
10
10
1
6
article
Oxford Univ. Press
Oxford
1
2020-01-17
2020-01-17
--
A new lineage of segmented RNA viruses infecting animals
Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.
Virus Evolution
10.1093/ve/vez061
2057-1577
vez061
Darren J. Obbard
2818949-8
<a href="https://doi.org/10.25932/publishup-51604">Zweitveröffentlichung in der Schriftenreihe Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1411</a>
false
false
CC-BY - Namensnennung 4.0 International
Darren J. Obbard
Mang Shi
Katherine E. Roberts
Ben Longdon
Alice B. Dennis
eng
uncontrolled
metagenome
eng
uncontrolled
RNA virus
eng
uncontrolled
dark virus
eng
uncontrolled
arthropod
eng
uncontrolled
RNA interference
Biowissenschaften; Biologie
Tiere (Zoologie)
Institut für Biochemie und Biologie
Referiert
Gold Open-Access
61405
2020
2020
eng
1
18
18
4
10
article
MDPI
Basel
1
2020-04-10
2020-04-10
--
Involvement of lactate and pyruvate in the anti-inflammatory effects exerted by voluntary activation of the sympathetic nervous system
We recently demonstrated that the sympathetic nervous system can be voluntarily activated following a training program consisting of cold exposure, breathing exercises, and meditation. This resulted in profound attenuation of the systemic inflammatory response elicited by lipopolysaccharide (LPS) administration. Herein, we assessed whether this training program affects the plasma metabolome and if these changes are linked to the immunomodulatory effects observed. A total of 224 metabolites were identified in plasma obtained from 24 healthy male volunteers at six timepoints, of which 98 were significantly altered following LPS administration. Effects of the training program were most prominent shortly after initiation of the acquired breathing exercises but prior to LPS administration, and point towards increased activation of the Cori cycle. Elevated concentrations of lactate and pyruvate in trained individuals correlated with enhanced levels of anti-inflammatory interleukin (IL)-10. In vitro validation experiments revealed that co-incubation with lactate and pyruvate enhances IL-10 production and attenuates the release of pro-inflammatory IL-1 beta and IL-6 by LPS-stimulated leukocytes. Our results demonstrate that practicing the breathing exercises acquired during the training program results in increased activity of the Cori cycle. Furthermore, this work uncovers an important role of lactate and pyruvate in the anti-inflammatory phenotype observed in trained subjects.
Metabolites
10.3390/metabo10040148
2218-1989
148
Matthijs Kox
2662251-8
<a href="https://doi.org/10.25932/publishup-51778">Zweitveröffentlichung in der Schriftenreihe Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1413</a>
CC-BY - Namensnennung 4.0 International
Jelle Zwaag
Rob ter Horst
Ivana Blaženović
Daniel Stößel
Jacqueline Ratter
Josephine M. Worseck
Nicolas Schauer
Rinke Stienstra
Mihai G. Netea
Dieter Jahn
Peter Pickkers
Matthijs Kox
eng
uncontrolled
metabolomics
eng
uncontrolled
LPS
eng
uncontrolled
endotoxin
eng
uncontrolled
pyruvate
eng
uncontrolled
lactate
eng
uncontrolled
cytokines
eng
uncontrolled
inflammation
eng
uncontrolled
human endotoxemia
eng
uncontrolled
cori cycle
eng
uncontrolled
warburg effect
Biowissenschaften; Biologie
Medizin und Gesundheit
Institut für Biochemie und Biologie
Referiert
Gold Open-Access
DOAJ gelistet
51778
2020
2020
eng
20
4
postprint
1
2020-04-10
2020-04-10
--
Involvement of lactate and pyruvate in the anti-inflammatory effects exerted by voluntary activation of the sympathetic nervous system
We recently demonstrated that the sympathetic nervous system can be voluntarily activated following a training program consisting of cold exposure, breathing exercises, and meditation. This resulted in profound attenuation of the systemic inflammatory response elicited by lipopolysaccharide (LPS) administration. Herein, we assessed whether this training program affects the plasma metabolome and if these changes are linked to the immunomodulatory effects observed. A total of 224 metabolites were identified in plasma obtained from 24 healthy male volunteers at six timepoints, of which 98 were significantly altered following LPS administration. Effects of the training program were most prominent shortly after initiation of the acquired breathing exercises but prior to LPS administration, and point towards increased activation of the Cori cycle. Elevated concentrations of lactate and pyruvate in trained individuals correlated with enhanced levels of anti-inflammatory interleukin (IL)-10. In vitro validation experiments revealed that co-incubation with lactate and pyruvate enhances IL-10 production and attenuates the release of pro-inflammatory IL-1 beta and IL-6 by LPS-stimulated leukocytes. Our results demonstrate that practicing the breathing exercises acquired during the training program results in increased activity of the Cori cycle. Furthermore, this work uncovers an important role of lactate and pyruvate in the anti-inflammatory phenotype observed in trained subjects.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-51778
urn:nbn:de:kobv:517-opus4-517784
1866-8372
online registration
publish
<a href="http://publishup.uni-potsdam.de/61405">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Metabolites 2020, 10(4), 148; https://doi.org/10.3390/metabo10040148
Version of Record
CC-BY - Namensnennung 4.0 International
Jelle Zwaag
Rob ter Horst
Ivana Blaženović
Daniel Stößel
Jacqueline Ratter
Josephine M. Worseck
Nicolas Schauer
Rinke Stienstra
Mihai G. Netea
Dieter Jahn
Peter Pickkers
Matthijs Kox
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1413
eng
uncontrolled
metabolomics
eng
uncontrolled
LPS
eng
uncontrolled
endotoxin
eng
uncontrolled
pyruvate
eng
uncontrolled
lactate
eng
uncontrolled
cytokines
eng
uncontrolled
inflammation
eng
uncontrolled
human endotoxemia
eng
uncontrolled
cori cycle
eng
uncontrolled
warburg effect
Biowissenschaften; Biologie
Medizin und Gesundheit
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51778/zmnr1413.pdf
51871
2020
2020
eng
13
3
postprint
1
2020-04-16
2020-04-16
--
Morphological differentiation in African weakly electric fish (genus Campylomormyrus) relates to substrate preferences
Under an ecological speciation scenario, the radiation of African weakly electric fish (genus Campylomormyrus) is caused by an adaptation to different food sources, associated with diversification of the electric organ discharge (EOD). This study experimentally investigates a phenotype-environment correlation to further support this scenario. Our behavioural experiments showed that three sympatric Campylomormyrus species with significantly divergent snout morphology differentially react to variation in substrate structure. While the short snout species (C. tamandua) exhibits preference to sandy substrate, the long snout species (C. rhynchophorus) significantly prefers a stone substrate for feeding. A third species with intermediate snout size (C. compressirostris) does not exhibit any substrate preference. This preference is matched with the observation that long-snouted specimens probe deeper into the stone substrate, presumably enabling them to reach prey more distant to the substrate surface. These findings suggest that the diverse feeding apparatus in the genus Campylomormyrus may have evolved in adaptation to specific microhabitats, i.e., substrate structures where these fish forage. Whether the parallel divergence in EOD is functionally related to this adaptation or solely serves as a prezygotic isolation mechanism remains to be elucidated.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-51871
urn:nbn:de:kobv:517-opus4-518714
1866-8372
online registration
publish
<a href="http://publishup.uni-potsdam.de/61400">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Evol Ecol 34, 427–437 (2020). https://doi.org/10.1007/s10682-020-10043-3
Version of Record
false
true
CC-BY - Namensnennung 4.0 International
Rahma Amen
Rebecca Nagel
Maximilian Hedt
Frank Kirschbaum
Ralph Tiedemann
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1416
eng
uncontrolled
ecological speciation
eng
uncontrolled
feeding behaviour
eng
uncontrolled
electric fish
eng
uncontrolled
trophic apparatus
eng
uncontrolled
evolutionary ecology
Biowissenschaften; Biologie
Tiere (Zoologie)
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51871/zmnr1416.pdf
61400
2020
2020
eng
427
437
11
3
34
article
Springer Science
Dordrecht
1
2020-04-16
2020-04-16
--
Morphological differentiation in African weakly electric fish (genus Campylomormyrus) relates to substrate preferences
Under an ecological speciation scenario, the radiation of African weakly electric fish (genus Campylomormyrus) is caused by an adaptation to different food sources, associated with diversification of the electric organ discharge (EOD). This study experimentally investigates a phenotype-environment correlation to further support this scenario. Our behavioural experiments showed that three sympatric Campylomormyrus species with significantly divergent snout morphology differentially react to variation in substrate structure. While the short snout species (C. tamandua) exhibits preference to sandy substrate, the long snout species (C. rhynchophorus) significantly prefers a stone substrate for feeding. A third species with intermediate snout size (C. compressirostris) does not exhibit any substrate preference. This preference is matched with the observation that long-snouted specimens probe deeper into the stone substrate, presumably enabling them to reach prey more distant to the substrate surface. These findings suggest that the diverse feeding apparatus in the genus Campylomormyrus may have evolved in adaptation to specific microhabitats, i.e., substrate structures where these fish forage. Whether the parallel divergence in EOD is functionally related to this adaptation or solely serves as a prezygotic isolation mechanism remains to be elucidated.
Evolutionary Ecology
10.1007/s10682-020-10043-3
0269-7653
1573-8477
Ralph Tiedemann
1497820-9
<a href="https://doi.org/10.25932/publishup-51871">Zweitveröffentlichung in der Schriftenreihe Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1416</a>
false
false
CC-BY - Namensnennung 4.0 International
Rahma Amen
Rebecca Nagel
Maximilian Hedt
Frank Kirschbaum
Ralph Tiedemann
eng
uncontrolled
ecological speciation
eng
uncontrolled
feeding behaviour
eng
uncontrolled
electric fish
eng
uncontrolled
trophic apparatus
eng
uncontrolled
evolutionary ecology
Biowissenschaften; Biologie
Tiere (Zoologie)
Institut für Biochemie und Biologie
Referiert
Gold Open-Access
62924
2022
2022
eng
11
1
12
article
Macmillan Publishers Limited, part of Springer Nature
London
1
2022-05-13
2022-05-13
--
The use of high-affinity polyhistidine binders as masking probes for the selection of an NDM-1 specific aptamer
The emergence of carbapenemase-producing multi-drug resistant Enterobacteriaceae poses a dramatic, world-wide health risk. Limited treatment options and a lack of easy-to-use methods for the detection of infections with multi-drug resistant bacteria leave the health-care system with a fast-growing challenge. Aptamers are single stranded DNA or RNA molecules that bind to their targets with high affinity and specificity and can therefore serve as outstanding detection probes. However, an effective aptamer selection process is often hampered by non-specific binding. When selections are carried out against recombinant proteins, purification tags (e.g. polyhistidine) serve as attractive side targets, which may impede protein target binding. In this study, aptamer selection was carried out against N-terminally hexa-histidine tagged New Delhi metallo-ss-lactamase 1. After 14 selection rounds binding to polyhistidine was detected rather than to New Delhi metallo-ss-lactamase 1. Hence, the selection strategy was changed. As one aptamer candidate showed remarkable binding affinity to polyhistidine, it was used as a masking probe and selection was restarted from selection round 10. Finally, after three consecutive selection rounds, an aptamer with specific binding properties to New Delhi metallo-ss-lactamase 1 was identified. This aptamer may serve as a much-needed detection probe for New Delhi metallo-ss-lactamase 1 expressing Enterobacteriaceae.
Scientific reports
10.1038/s41598-022-12062-2
35562409
2045-2322
outputup:dataSource:WoS:2022
7936
WOS:000803217300005
Menger, MM (corresponding author), Fraunhofer Inst Cell Therapy & Immunol, Branch Bioanalyt & Bioproc IZI BB, Muhlenberg 13, D-14476 Potsdam, Germany., marcus.menger@IZI-BB.fraunhofer.de
Projekt DEAL
Menger, Marcus M.
2024-03-11T09:11:22+00:00
sword
importub
filename=package.tar
d0c761a6af3b7ce59e47a107d0367375
false
true
CC-BY - Namensnennung 4.0 International
Wiebke Sabrowski
Nico Dreymann
Anja Möller
Denise Czepluch
Patricia P. Albani
Dimitrios Theodoridis
Marcus M. Menger
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
61501
2020
2020
eng
1
12
12
1795
10
article
Frontiers Media
Lausanne
1
2020-02-07
2020-02-07
--
Looking At the Past and Heading to the Future
In June 2019, more than a hundred plant researchers met in Cologne, Germany, for the 6th European Workshop on Plant Chromatin (EWPC). This conference brought together a highly dynamic community of researchers with the common aim to understand how chromatin organization controls gene expression, development, and plant responses to the environment. New evidence showing how epigenetic states are set, perpetuated, and inherited were presented, and novel data related to the three-dimensional organization of chromatin within the nucleus were discussed. At the level of the nucleosome, its composition by different histone variants and their specialized histone deposition complexes were addressed as well as the mechanisms involved in histone post-translational modifications and their role in gene expression. The keynote lecture on plant DNA methylation by Julie Law (SALK Institute) and the tribute session to Lars Hennig, honoring the memory of one of the founders of the EWPC who contributed to promote the plant chromatin and epigenetic field in Europe, added a very special note to this gathering. In this perspective article we summarize some of the most outstanding data and advances on plant chromatin research presented at this workshop.
Frontiers in Plant Science
Meeting Summary of the 6th European Workshop on Plant Chromatin 2019 in Cologne, Germany
10.3389/fpls.2019.01795
1664-462X
1795
Sara Farrona
2613694-6
<a href="https://doi.org/10.25932/publishup-51194">Zweitveröffentlichung in der Schriftenreihe Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1423</a>
CC-BY - Namensnennung 4.0 International
Jordi Moreno-Romero
Aline V. Probst
Inês Trindade
Kalyanikrishna
Julia Engelhorn
Sara Farrona
eng
uncontrolled
EWPC2019
eng
uncontrolled
chromatin
eng
uncontrolled
epigenetics
eng
uncontrolled
transcription
eng
uncontrolled
nucleus
Biowissenschaften; Biologie
Pflanzen (Botanik)
Institut für Biochemie und Biologie
Referiert
Gold Open-Access
DOAJ gelistet
51194
2020
2020
eng
14
postprint
1
2020-02-07
2020-02-07
--
Looking At the Past and Heading to the Future
In June 2019, more than a hundred plant researchers met in Cologne, Germany, for the 6th European Workshop on Plant Chromatin (EWPC). This conference brought together a highly dynamic community of researchers with the common aim to understand how chromatin organization controls gene expression, development, and plant responses to the environment. New evidence showing how epigenetic states are set, perpetuated, and inherited were presented, and novel data related to the three-dimensional organization of chromatin within the nucleus were discussed. At the level of the nucleosome, its composition by different histone variants and their specialized histone deposition complexes were addressed as well as the mechanisms involved in histone post-translational modifications and their role in gene expression. The keynote lecture on plant DNA methylation by Julie Law (SALK Institute) and the tribute session to Lars Hennig, honoring the memory of one of the founders of the EWPC who contributed to promote the plant chromatin and epigenetic field in Europe, added a very special note to this gathering. In this perspective article we summarize some of the most outstanding data and advances on plant chromatin research presented at this workshop.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
Meeting Summary of the 6th European Workshop on Plant Chromatin 2019 in Cologne, Germany
10.25932/publishup-51194
urn:nbn:de:kobv:517-opus4-511942
1866-8372
online registration
publish
<a href="http://publishup.uni-potsdam.de/61501">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Front. Plant Sci. 10:1795. doi: 10.3389/fpls.2019.01795
Version of Record
false
true
CC-BY - Namensnennung 4.0 International
Jordi Moreno-Romero
Aline V. Probst
Inês Trindade
Kalyanikrishna
Julia Engelhorn
Sara Farrona
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1423
eng
uncontrolled
EWPC2019
eng
uncontrolled
chromatin
eng
uncontrolled
epigenetics
eng
uncontrolled
transcription
eng
uncontrolled
nucleus
Biowissenschaften; Biologie
Pflanzen (Botanik)
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51194/zmnr1423.pdf
51243
2020
2020
eng
19
1
postprint
1
2020-01-22
2020-01-22
--
A taxonomically harmonized and temporally standardized fossil pollen dataset from Siberia covering the last 40 kyr
Pollen records from Siberia are mostly absent in global or Northern Hemisphere synthesis works. Here we present a taxonomically harmonized and temporally standardized pollen dataset that was synthesized using 173 palynological records from Siberia and adjacent areas (northeastern Asia, 42-75 degrees N, 50-180 degrees E). Pollen data were taxonomically harmonized, i.e. the original 437 taxa were assigned to 106 combined pollen taxa. Age-depth models for all records were revised by applying a constant Bayesian age-depth modelling routine. The pollen dataset is available as count data and percentage data in a table format (taxa vs. samples), with age information for each sample. The dataset has relatively few sites covering the last glacial period between 40 and 11.5 ka (calibrated thousands of years before 1950 CE) particularly from the central and western part of the study area. In the Holocene period, the dataset has many sites from most of the area, with the exception of the central part of Siberia. Of the 173 pollen records, 81 % of pollen counts were downloaded from open databases (GPD, EPD, PANGAEA) and 10 % were contributions by the original data gatherers, while a few were digitized from publications. Most of the pollen records originate from peatlands (48 %) and lake sediments (33 %). Most of the records (83 %) have >= 3 dates, allowing the establishment of reliable chronologies. The dataset can be used for various purposes, including pollen data mapping (example maps for Larix at selected time slices are shown) as well as quantitative climate and vegetation reconstructions. The datasets for pollen counts and pollen percentages are available at https://doi.org/10.1594/PANGAEA.898616 (Cao et al., 2019a), also including the site information, data source, original publication, dating data, and the plant functional type for each pollen taxa.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-51243
urn:nbn:de:kobv:517-opus4-512438
1866-8372
online registration
publish
<a href="http://publishup.uni-potsdam.de/61539">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Earth Syst. Sci. Data, 12, 119–135, 2020 https://doi.org/10.5194/essd-12-119-2020
Version of Record
false
true
CC-BY - Namensnennung 4.0 International
Xianyong Cao
Fang Tian
Andrei Andreev
Patricia M. Anderson
Anatoly V. Lozhkin
Elena Bezrukova
Jian Ni
Natalia Rudaya
Astrid Stobbe
Mareike Wieczorek
Ulrike Herzschuh
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1427
eng
uncontrolled
Late Quaternary vegetation
eng
uncontrolled
Holocene environmental history
eng
uncontrolled
eastern continental Asia
eng
uncontrolled
plant macrofossil data
eng
uncontrolled
late pleistocene
eng
uncontrolled
paleoenvironmental records
eng
uncontrolled
Verkhoyansk mountains
eng
uncontrolled
climate dynamics
eng
uncontrolled
glacial maximum
eng
uncontrolled
Northern Asia
Geowissenschaften
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Institut für Umweltwissenschaften und Geographie
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51243/zmnr1427.pdf
61539
2020
2020
eng
119
135
17
1
12
article
Copernics Publications
Katlenburg-Lindau
1
2020-01-22
2020-01-22
--
A taxonomically harmonized and temporally standardized fossil pollen dataset from Siberia covering the last 40 kyr
Pollen records from Siberia are mostly absent in global or Northern Hemisphere synthesis works. Here we present a taxonomically harmonized and temporally standardized pollen dataset that was synthesized using 173 palynological records from Siberia and adjacent areas (northeastern Asia, 42-75 degrees N, 50-180 degrees E). Pollen data were taxonomically harmonized, i.e. the original 437 taxa were assigned to 106 combined pollen taxa. Age-depth models for all records were revised by applying a constant Bayesian age-depth modelling routine. The pollen dataset is available as count data and percentage data in a table format (taxa vs. samples), with age information for each sample. The dataset has relatively few sites covering the last glacial period between 40 and 11.5 ka (calibrated thousands of years before 1950 CE) particularly from the central and western part of the study area. In the Holocene period, the dataset has many sites from most of the area, with the exception of the central part of Siberia. Of the 173 pollen records, 81 % of pollen counts were downloaded from open databases (GPD, EPD, PANGAEA) and 10 % were contributions by the original data gatherers, while a few were digitized from publications. Most of the pollen records originate from peatlands (48 %) and lake sediments (33 %). Most of the records (83 %) have >= 3 dates, allowing the establishment of reliable chronologies. The dataset can be used for various purposes, including pollen data mapping (example maps for Larix at selected time slices are shown) as well as quantitative climate and vegetation reconstructions. The datasets for pollen counts and pollen percentages are available at https://doi.org/10.1594/PANGAEA.898616 (Cao et al., 2019a), also including the site information, data source, original publication, dating data, and the plant functional type for each pollen taxa.
Earth System Science Data
10.5194/essd-12-119-2020
1866-3508
1866-3516
Herzschuh, Ulrike
Cao, Xianyong
2475469-9
<a href="https://doi.org/10.25932/publishup-51243">Zweitveröffentlichung in der Schriftenreihe Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1427</a>
false
false
CC-BY - Namensnennung 4.0 International
Xianyong Cao
Fang Tian
Andrei Andreev
Patricia M. Anderson
Anatoly V. Lozhkin
Elena Bezrukova
Jian Ni
Natalia Rudaya
Astrid Stobbe
Mareike Wieczorek
Ulrike Herzschuh
eng
uncontrolled
Late Quaternary vegetation
eng
uncontrolled
Holocene environmental history
eng
uncontrolled
eastern continental Asia
eng
uncontrolled
plant macrofossil data
eng
uncontrolled
late pleistocene
eng
uncontrolled
paleoenvironmental records
eng
uncontrolled
Verkhoyansk mountains
eng
uncontrolled
climate dynamics
eng
uncontrolled
glacial maximum
eng
uncontrolled
Northern Asia
Geowissenschaften
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Institut für Umweltwissenschaften und Geographie
Gold Open-Access
62926
2021
eng
21
1
22
article
BioMed Central
London
1
2021-06-16
2021-06-16
--
Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa
Background
Secondary endosymbionts of aphids provide benefits to their hosts, but also impose costs such as reduced lifespan and reproductive output. The aphid Aphis fabae is host to different strains of the secondary endosymbiont Hamiltonella defensa, which encode different putative toxins. These strains have very different phenotypes: They reach different densities in the host, and the costs and benefits (protection against parasitoid wasps) they confer to the host vary strongly.
Results
We used RNA-Seq to generate hypotheses on why four of these strains inflict such different costs to A. fabae. We found different H. defensa strains to cause strain-specific changes in aphid gene expression, but little effect of H. defensa on gene expression of the primary endosymbiont, Buchnera aphidicola. The highly costly and over-replicating H. defensa strain H85 was associated with strongly reduced aphid expression of hemocytin, a marker of hemocytes in Drosophila. The closely related strain H15 was associated with downregulation of ubiquitin-related modifier 1, which is related to nutrient-sensing and oxidative stress in other organisms. Strain H402 was associated with strong differential regulation of a set of hypothetical proteins, the majority of which were only differentially regulated in presence of H402.
Conclusions
Overall, our results suggest that costs of different strains of H. defensa are likely caused by different mechanisms, and that these costs are imposed by interacting with the host rather than the host's obligatory endosymbiont B. aphidicola.
BMC genomics
10.1186/s12864-021-07742-8
34134631
1471-2164
outputup:dataSource:WoS:2021
449
WOS:000664622000001
Kaech, Heidi (corresponding author), Swiss Fed Inst Aquat Sci & Technol, Eawag, Aquat Ecol, Dubendorf, Switzerland.; Kaech, H (corresponding author), Swiss Fed Inst Technol, Dept Environm Syst Sci, D USYS, Zurich, Switzerland., kaechh@outlook.com
Swiss National Science FoundationSwiss National Science Foundation (SNSF)European Commission [CRSII3_154396]
Kaech, Heidi
2024-03-11T09:39:26+00:00
sword
importub
filename=package.tar
dfd1ae925bbd27b35f57cd1eb3d6fb86
false
true
CC-BY - Namensnennung 4.0 International
Heidi Kaech
Alice B. Dennis
Christoph Vorburger
eng
uncontrolled
Aphis fabae
eng
uncontrolled
Buchnera
eng
uncontrolled
Cost of resistance
eng
uncontrolled
Hamiltonella
eng
uncontrolled
Host-symbiont interaction
eng
uncontrolled
RNA-Seq
eng
uncontrolled
Symbiosis
Biowissenschaften; Biologie
Medizin und Gesundheit
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
51652
2020
2020
eng
15
5-6
postprint
1
2020-04-13
2020-04-13
--
Tissue-specific epigenetic inheritance after paternal heat exposure in male wild guinea pigs
External temperature change has been shown to modify epigenetic patterns, such as DNA methylation, which regulates gene expression. DNA methylation is heritable, and as such provides a mechanism to convey environmental information to subsequent generations. Studies on epigenetic response to temperature increase are still scarce in wild mammals, even more so studies that compare tissue-specific epigenetic responses. Here, we aim to address differential epigenetic responses on a gene and gene pathway level in two organs, liver and testis. We chose these organs, because the liver is the main metabolic and thermoregulation organ, and epigenetic modifications in testis are potentially transmitted to the F2 generation. We focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to an ambient temperature increase of 10 degrees C, and investigated differential methylated regions of sons sired before and after the paternal exposure using Reduced Representation Bisulfite Sequencing. We detected both a highly tissue-specific epigenetic response, reflected in genes involved in organ-specific metabolic pathways, and a more general regulation of single genes epigenetically modified in both organs. We conclude that genomes are context-specifically differentially epigenetically regulated in response to temperature increase. These findings emphasize the epigenetic relevance in cell differentiation, which is essential for the specific function(s) of complex organs, and is represented in a diverse molecular regulation of genes and gene pathways. The results also emphasize the paternal contribution to adaptive processes.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-51652
urn:nbn:de:kobv:517-opus4-516525
1866-8372
32285146
online registration
publish
<a href="http://publishup.uni-potsdam.de/58368">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Mammalian genome 31 (2020) 5-6, pp. 157 - 169. https://doi.org/10.1007/s00335-020-09832-6
Version of Record
false
true
CC-BY - Namensnennung 4.0 International
Alexandra Weyrich
Selma Yasar
Dorina Lenz
Jörns Fickel
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1431
eng
uncontrolled
DNA methylation
eng
uncontrolled
gene-expression
eng
uncontrolled
CPG Islands
eng
uncontrolled
stress
eng
uncontrolled
hyperthermia
eng
uncontrolled
testis
Biowissenschaften; Biologie
Tiere (Zoologie)
Medizin und Gesundheit
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51652/zmnr1431.pdf
51653
2020
2020
eng
26
6
postprint
1
2020-04-10
2020-04-10
--
Functional features of Trehalose-6-Phosphate Synthase 1
Tre6P synthesis by TPS1 is essential for embryogenesis and postembryonic growth in Arabidopsis, and appropriate Suc signaling by Tre6P is dependent on the noncatalytic domains of TPS1. In Arabidopsis (Arabidopsis thaliana), TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) catalyzes the synthesis of the sucrose-signaling metabolite trehalose 6-phosphate (Tre6P) and is essential for embryogenesis and normal postembryonic growth and development. To understand its molecular functions, we transformed the embryo-lethal tps1-1 null mutant with various forms of TPS1 and with a heterologous TPS (OtsA) from Escherichia coli, under the control of the TPS1 promoter, and tested for complementation. TPS1 protein localized predominantly in the phloem-loading zone and guard cells in leaves, root vasculature, and shoot apical meristem, implicating it in both local and systemic signaling of Suc status. The protein is targeted mainly to the nucleus. Restoring Tre6P synthesis was both necessary and sufficient to rescue the tps1-1 mutant through embryogenesis. However, postembryonic growth and the sucrose-Tre6P relationship were disrupted in some complementation lines. A point mutation (A119W) in the catalytic domain or truncating the C-terminal domain of TPS1 severely compromised growth. Despite having high Tre6P levels, these plants never flowered, possibly because Tre6P signaling was disrupted by two unidentified disaccharide-monophosphates that appeared in these plants. The noncatalytic domains of TPS1 ensure its targeting to the correct subcellular compartment and its catalytic fidelity and are required for appropriate signaling of Suc status by Tre6P.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
an essential enzyme in Arabidopsis
10.25932/publishup-51653
urn:nbn:de:kobv:517-opus4-516532
1866-8372
online registration
publish
<a href="http://publishup.uni-potsdam.de/61604">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
The Plant Cell, Volume 32, Issue 6, June 2020, Pages 1949–1972, https://doi.org/10.1105/tpc.19.00837
Version of Record
false
true
CC-BY - Namensnennung 4.0 International
Franziska Fichtner
Justyna Jadwiga Olas
Regina Feil
Mutsumi Watanabe
Ursula Krause
Rainer Hoefgen
Mark Stitt
John Edward Lunn
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1432
eng
uncontrolled
cyanobacterial sucrose-phosphatase
eng
uncontrolled
trehalose 6-phosphate
eng
uncontrolled
vegetative growth
eng
uncontrolled
crystal-structure
eng
uncontrolled
gene-expression
eng
uncontrolled
thaliana
eng
uncontrolled
metabolism
eng
uncontrolled
phosphorylation
eng
uncontrolled
reveals
eng
uncontrolled
proteins
Biowissenschaften; Biologie
Pflanzen (Botanik)
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51653/zmnr1432.pdf
61604
2020
2020
eng
1949
1972
24
6
32
article
Oxford University Press
Oxford
1
2020-04-10
2020-04-10
--
Functional features of Trehalose-6-Phosphate Synthase 1
Tre6P synthesis by TPS1 is essential for embryogenesis and postembryonic growth in Arabidopsis, and appropriate Suc signaling by Tre6P is dependent on the noncatalytic domains of TPS1. In Arabidopsis (Arabidopsis thaliana), TREHALOSE-6-PHOSPHATE SYNTHASE1 (TPS1) catalyzes the synthesis of the sucrose-signaling metabolite trehalose 6-phosphate (Tre6P) and is essential for embryogenesis and normal postembryonic growth and development. To understand its molecular functions, we transformed the embryo-lethal tps1-1 null mutant with various forms of TPS1 and with a heterologous TPS (OtsA) from Escherichia coli, under the control of the TPS1 promoter, and tested for complementation. TPS1 protein localized predominantly in the phloem-loading zone and guard cells in leaves, root vasculature, and shoot apical meristem, implicating it in both local and systemic signaling of Suc status. The protein is targeted mainly to the nucleus. Restoring Tre6P synthesis was both necessary and sufficient to rescue the tps1-1 mutant through embryogenesis. However, postembryonic growth and the sucrose-Tre6P relationship were disrupted in some complementation lines. A point mutation (A119W) in the catalytic domain or truncating the C-terminal domain of TPS1 severely compromised growth. Despite having high Tre6P levels, these plants never flowered, possibly because Tre6P signaling was disrupted by two unidentified disaccharide-monophosphates that appeared in these plants. The noncatalytic domains of TPS1 ensure its targeting to the correct subcellular compartment and its catalytic fidelity and are required for appropriate signaling of Suc status by Tre6P.
The Plant Cell
an essential enzyme in Arabidopsis
10.1105/tpc.19.00837
0032-0781
1471-9053
John Edward Lunn
International Max Planck Research School, Primary Metabolism and Plant Growth; Max Planck Society
2020758-X
<a href="https://doi.org/10.25932/publishup-51653">Zweitveröffentlichung in der Schriftenreihe Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1432</a>
CC-BY - Namensnennung 4.0 International
Franziska Fichtner
Justyna Jadwiga Olas
Regina Feil
Mutsumi Watanabe
Ursula Krause
Rainer Hoefgen
Mark Stitt
John Edward Lunn
eng
uncontrolled
cyanobacterial sucrose-phosphatase
eng
uncontrolled
trehalose 6-phosphate
eng
uncontrolled
vegetative growth
eng
uncontrolled
crystal-structure
eng
uncontrolled
gene-expression
eng
uncontrolled
thaliana
eng
uncontrolled
metabolism
eng
uncontrolled
phosphorylation
eng
uncontrolled
reveals
eng
uncontrolled
proteins
Biowissenschaften; Biologie
Pflanzen (Botanik)
Institut für Biochemie und Biologie
Referiert
Hybrid Open-Access
51655
2020
2020
eng
22
6
postprint
1
2020-04-01
2020-04-01
--
The biosynthesis of the molybdenum cofactors in Escherichia coli
The biosynthesis of the molybdenum cofactor (Moco) is highly conserved among all kingdoms of life. In all molybdoenzymes containing Moco, the molybdenum atom is coordinated to a dithiolene group present in the pterin-based 6-alkyl side chain of molybdopterin (MPT). In general, the biosynthesis of Moco can be divided into four steps in in bacteria: (i) the starting point is the formation of the cyclic pyranopterin monophosphate (cPMP) from 5 '-GTP, (ii) in the second step the two sulfur atoms are inserted into cPMP leading to the formation of MPT, (iii) in the third step the molybdenum atom is inserted into MPT to form Moco and (iv) in the fourth step bis-Mo-MPT is formed and an additional modification of Moco is possible with the attachment of a nucleotide (CMP or GMP) to the phosphate group of MPT, forming the dinucleotide variants of Moco. This review presents an update on the well-characterized Moco biosynthesis in the model organism Escherichia coli including novel discoveries from the recent years.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-51655
urn:nbn:de:kobv:517-opus4-516559
1866-8372
32239579
online registration
publish
<a href="http://publishup.uni-potsdam.de/56228">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Environ Microbiol. (2020) 22(6), 2007–2026. https://doi.org/10.1111/1462-2920.15003
Version of Record
false
true
CC-BY - Namensnennung 4.0 International
Silke Leimkühler
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1433
eng
uncontrolled
periplasmic nitrate reductase
eng
uncontrolled
biotin sulfoxide reductase
eng
uncontrolled
in-vitro-synthesis
eng
uncontrolled
n-oxide reductase
eng
uncontrolled
crystal-structure
eng
uncontrolled
molybdopterin synthase
eng
uncontrolled
formate dehydrogenase
eng
uncontrolled
rhodobacter-capsulatus
eng
uncontrolled
xanthine dehydrogenase
eng
uncontrolled
converting factor
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51655/zmnr1433.pdf
61745
2020
2020
eng
445
456
12
4
129
article
Wiley-Blackwell
Oxford
1
2020-01-31
2020-01-31
--
Resilience trinity
Ensuring ecosystem resilience is an intuitive approach to safeguard the functioning of ecosystems and hence the future provisioning of ecosystem services (ES). However, resilience is a multi-faceted concept that is difficult to operationalize. Focusing on resilience mechanisms, such as diversity, network architectures or adaptive capacity, has recently been suggested as means to operationalize resilience. Still, the focus on mechanisms is not specific enough. We suggest a conceptual framework, resilience trinity, to facilitate management based on resilience mechanisms in three distinctive decision contexts and time-horizons: 1) reactive, when there is an imminent threat to ES resilience and a high pressure to act, 2) adjustive, when the threat is known in general but there is still time to adapt management and 3) provident, when time horizons are very long and the nature of the threats is uncertain, leading to a low willingness to act. Resilience has different interpretations and implications at these different time horizons, which also prevail in different disciplines. Social ecology, ecology and engineering are often implicitly focussing on provident, adjustive or reactive resilience, respectively, but these different notions of resilience and their corresponding social, ecological and economic tradeoffs need to be reconciled. Otherwise, we keep risking unintended consequences of reactive actions, or shying away from provident action because of uncertainties that cannot be reduced. The suggested trinity of time horizons and their decision contexts could help ensuring that longer-term management actions are not missed while urgent threats to ES are given priority.
Oikos
safeguarding ecosystem functioning and services across three different time horizons and decision contexts
10.1111/oik.07213
0030-1299
1600-0706
<a href="https://doi.org/10.25932/publishup-51528">Zweitveröffentlichung in der Schriftenreihe Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe ; 1444</a>
Grimm, Volker
German Research Foundation DFG project TI 824/2-1; UFZ’s Integrated Project ‘Emerging Ecosystems; Terrestrial Environment’ of the Helmholtz Association
2025658-9
false
false
CC-BY - Namensnennung 4.0 International
Hanna Weise
Harald Auge
Cornelia Baessler
Ilona Bärlund
Elena M. Bennett
Uta Berger
Friedrich Bohn
Aletta Bonn
Dietrich Borchardt
Fridolin Brand
Florian Jeltsch
Jasmin Radha Joshi
Volker Grimm
eng
uncontrolled
concepts
eng
uncontrolled
ecosystems
eng
uncontrolled
ecosystem services provisioning
eng
uncontrolled
management
eng
uncontrolled
resilience
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Gold Open-Access
51528
2020
2020
eng
14
4
postprint
1
2020-01-31
2020-01-31
--
Resilience trinity
Ensuring ecosystem resilience is an intuitive approach to safeguard the functioning of ecosystems and hence the future provisioning of ecosystem services (ES). However, resilience is a multi-faceted concept that is difficult to operationalize. Focusing on resilience mechanisms, such as diversity, network architectures or adaptive capacity, has recently been suggested as means to operationalize resilience. Still, the focus on mechanisms is not specific enough. We suggest a conceptual framework, resilience trinity, to facilitate management based on resilience mechanisms in three distinctive decision contexts and time-horizons: 1) reactive, when there is an imminent threat to ES resilience and a high pressure to act, 2) adjustive, when the threat is known in general but there is still time to adapt management and 3) provident, when time horizons are very long and the nature of the threats is uncertain, leading to a low willingness to act. Resilience has different interpretations and implications at these different time horizons, which also prevail in different disciplines. Social ecology, ecology and engineering are often implicitly focussing on provident, adjustive or reactive resilience, respectively, but these different notions of resilience and their corresponding social, ecological and economic tradeoffs need to be reconciled. Otherwise, we keep risking unintended consequences of reactive actions, or shying away from provident action because of uncertainties that cannot be reduced. The suggested trinity of time horizons and their decision contexts could help ensuring that longer-term management actions are not missed while urgent threats to ES are given priority.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
Safeguarding ecosystem functioning and services across three different time horizons and decision contexts
10.25932/publishup-51528
urn:nbn:de:kobv:517-opus4-515284
1866-8372
online registration
publish
<a href="http://publishup.uni-potsdam.de/61745">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Oikos, 129: 445-456. https://doi.org/10.1111/oik.07213
Version of Record
false
true
CC-BY - Namensnennung 4.0 International
Hanna Weise
Harald Auge
Cornelia Baessler
Ilona Bärlund
Elena M. Bennett
Uta Berger
Friedrich Bohn
Aletta Bonn
Dietrich Borchardt
Fridolin Brand
Florian Jeltsch
Jasmin Radha Joshi
Volker Grimm
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1444
eng
uncontrolled
concepts
eng
uncontrolled
ecosystems
eng
uncontrolled
ecosystem services provisioning
eng
uncontrolled
management
eng
uncontrolled
resilience
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51528/zmnr1444.pdf
60096
2021
2021
eng
773
773
1
6
207
article
Springer
Heidelberg
1
2021-10-17
2021-07-24
--
Correction to: Intragenus F1-hybrids of African weakly electric fish (Mormyridae: Campylomormyrus tamandua male x C. compressirostris female) are fertile (vol 206, pg 571, 2020)
Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology
10.1007/s00359-021-01513-2
34657165
0340-7594
1432-1351
outputup:dataSource:PubMed:2021
WOS:000708220600001
Kirschbaum, F (corresponding author), Humboldt Univ, Albrecht Daniel Thaer Inst Agr & Hort Sci, Fac Life Sci, Unit Biol & Ecol Fishes, Philippstr 13,Haus 16, D-10115 Berlin, Germany., frank.kirschbaum@staff.hu-berlin.de
2023-07-24T12:13:10+00:00
sword
importub
filename=package.tar
377b678e6e5a1c70bed31b89f23ac82a
1459295-2
231244-X
Kirschbaum, Frank
Originalartikel: https://doi.org/10.1007/s00359-020-01425-7
false
true
CC-BY - Namensnennung 4.0 International
Yevheniia Korniienko
Linh Nguyen
Stephanie Baumgartner
Marianne Vater
Ralph Tiedemann
Frank Kirschbaum
Medizin und Gesundheit
Institut für Biochemie und Biologie
Referiert
Import
62897
2022
2022
eng
2699
2712
14
20
review
Research Network of Computational and Structural Biotechnology (RNCSB)
Gotenburg
1
2022-06-01
2022-06-01
--
Computational identification of protein complexes from network interactions: Present state, challenges, and the way forward
Physically interacting proteins form macromolecule complexes that drive diverse cellular processes. Advances in experimental techniques that capture interactions between proteins provide us with protein-protein interaction (PPI) networks from several model organisms. These datasets have enabled the prediction and other computational analyses of protein complexes. Here we provide a systematic review of the state-of-the-art algorithms for protein complex prediction from PPI networks proposed in the past two decades. The existing approaches that solve this problem are categorized into three groups, including: cluster-quality-based, node affinity-based, and network embedding-based approaches, and we compare and contrast the advantages and disadvantages. We further include a comparative analysis by computing the performance of eighteen methods based on twelve well-established performance measures on four widely used benchmark protein-protein interaction networks. Finally, the limitations and drawbacks of both, current data and approaches, along with the potential solutions in this field are discussed, with emphasis on the points that pave the way for future research efforts in this field. (c) 2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).
Computational and structural biotechnology journal
present state, challenges, and the way forward
10.1016/j.csbj.2022.05.049
35685359
2001-0370
outputup:dataSource:WoS:2022
WOS:000808300900007
Nikoloski, Z (corresponding author), Univ Potsdam, Inst Biochem & Biol, Bioinformat, D-14476 Potsdam, Germany.; Nikoloski, Z (corresponding author), Max Planck Inst Mol Plant Physiol, Syst Biol & Math Modeling, D-14476 Potsdam, Germany., Nikoloski@mpimp-golm.mpg.de
Bavarian State Ministry for Economic Affairs Regional Development and; Energy [07 02/683 87/19/21/19/22/20/23]; Max-Planck Gesellschaft (MPG);; Max Planck Institute of Molecular Plant Physiology (MPIMP)
Nikoloski, Zoran
2024-03-07T10:21:14+00:00
sword
importub
filename=package.tar
402522a5ed156740eac78a4bc2f3ff62
false
true
CC-BY - Namensnennung 4.0 International
Sara Omranian
Zoran Nikoloski
Dominik G. Grimm
eng
uncontrolled
Protein Complex Prediction
eng
uncontrolled
Protein-Protein interaction network
eng
uncontrolled
Network
eng
uncontrolled
Clustering Algorithms
eng
uncontrolled
Network embedding
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62883
2022
2022
eng
11
10
article
Frontiers Media
Lausanne
1
2022-04-28
2022-04-28
--
A Cell-free Expression Pipeline for the Generation and Functional Characterization of Nanobodies
Cell-free systems are well-established platforms for the rapid synthesis, screening, engineering and modification of all kinds of recombinant proteins ranging from membrane proteins to soluble proteins, enzymes and even toxins. Also within the antibody field the cell-free technology has gained considerable attention with respect to the clinical research pipeline including antibody discovery and production. Besides the classical full-length monoclonal antibodies (mAbs), so-called "nanobodies" (Nbs) have come into focus. A Nb is the smallest naturally-derived functional antibody fragment known and represents the variable domain (VHH, similar to 15 kDa) of a camelid heavy-chain-only antibody (HCAb). Based on their nanoscale and their special structure, Nbs display striking advantages concerning their production, but also their characteristics as binders, such as high stability, diversity, improved tissue penetration and reaching of cavity-like epitopes. The classical way to produce Nbs depends on the use of living cells as production host. Though cell-based production is well-established, it is still time-consuming, laborious and hardly amenable for high-throughput applications. Here, we present for the first time to our knowledge the synthesis of functional Nbs in a standardized mammalian cell-free system based on Chinese hamster ovary (CHO) cell lysates. Cell-free reactions were shown to be time-efficient and easy-to-handle allowing for the "on demand" synthesis of Nbs. Taken together, we complement available methods and demonstrate a promising new system for Nb selection and validation.
Frontiers in Bioengineering and Biotechnology
10.3389/fbioe.2022.896763
35573250
2296-4185
outputup:dataSource:WoS:2022
896763
WOS:000794317900001
Kubick, S (corresponding author), Fraunhofer Inst Cell Therapy & Immunol IZI, Branch Bioanalyt & Bioproc IZI BB, Potsdam, Germany.; Kubick, S (corresponding author), Free Univ Berlin, Inst Chem & Biochem, Berlin, Germany.; Kubick, S (corresponding author), Brandenburg Univ Technol Cottbus Senftenberg, Joint Fac, Fac Hlth Sci, Brandenburg Med Sch Theodor Fontane, Potsdam, Germany.; Kubick, S (corresponding author), Univ Potsdam, Potsdam, Germany., Stefan.Kubick@izi-bb.fraunhofer.de
Kubick, Stefan
2024-03-06T14:01:39+00:00
sword
importub
filename=package.tar
820ff070ee5b8e830b15a8dfdae44968
false
true
CC-BY - Namensnennung 4.0 International
Lisa Haueis
Marlitt Stech
Stefan Kubick
eng
uncontrolled
cell-free protein synthesis
eng
uncontrolled
In vitro transcription
eng
uncontrolled
translation
eng
uncontrolled
nanobody
eng
uncontrolled
VHH
eng
uncontrolled
camelid
eng
uncontrolled
CHO cell lysate
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62847
2021
2021
eng
14
303
article
Elsevier Science
Amsterdam [u.a.]
1
2020-11-19
2021-02-01
--
Developmental stage-specific metabolite signatures in Arabidopsis thaliana under optimal and mild nitrogen limitation
Metabolites influence flowering time, and thus are among the major determinants of yield. Despite the reported role of trehalose 6-phosphate and nitrate signaling on the transition from the vegetative to the reproductive phase, little is known about other metabolites contributing and responding to developmental phase changes. To increase our understanding which metabolic traits change throughout development in Arabidopsis thaliana and to identify metabolic markers for the vegetative and reproductive phases, especially among individual amino acids (AA), we profiled metabolites of plants grown in optimal (ON) and limited nitrogen (N) (LN) conditions, the latter providing a mild but consistent limitation of N. We found that although LN plants adapt their growth to a decreased level of N, their metabolite profiles are strongly distinct from ON plant profiles, with N as the driving factor for the observed differences. We demonstrate that the vegetative and the reproductive phase are not only marked by growth parameters such as biomass and rosette area, but also by specific metabolite signatures including specific single AA. In summary, we identified N-dependent and -independent indicators manifesting developmental stages, indicating that the plant's metabolic status also reports on the developmental phases.
Plant science : an international journal of experimental plant biology
10.1016/j.plantsci.2020.110746
33487337
0168-9452
1873-2259
outputup:dataSource:PubMed:2021
110746
WOS:000614154500004
Wahl, Vanessa (corresponding author), Max Planck Inst Mol Plant Physiol, Potsdam, Germany.; Olas, JJ (corresponding author), Univ Potsdam, Potsdam, Germany., olas@uni-potsdam.de; apelt@mpimp-golm.mpg.de; mutsumi@bs.naist.jp; <br /> hoefgen@mpimp-golm.mpg.de; vanessa.wahl@mpimp-golm.mpg.de
BMBFFederal Ministry of Education & Research (BMBF) [031B0191]; DFGGerman Research Foundation (DFG)European Commission [SPP1530, WA3639/1-2, WA3639/2-1]; Max Planck SocietyMax Planck SocietyFoundation CELLEX
Olas, Justyna Jadwiga
2024-03-01T11:18:24+00:00
sword
importub
filename=package.tar
db696f461146941cd899b442413dacd5
Wahl, Vanessa
false
true
CC-BY-NC-ND - Namensnennung, nicht kommerziell, keine Bearbeitungen 4.0 International
Justyna Jadwiga Olas
Federico Apelt
Mutsumi Watanabe
Rainer Höfgen
Vanessa Wahl
eng
uncontrolled
Amino acids
eng
uncontrolled
Floral induction
eng
uncontrolled
Flowering time
eng
uncontrolled
Nitrogen
eng
uncontrolled
Metabolites
eng
uncontrolled
Vegetative phase
eng
uncontrolled
Reproductive phase
Biowissenschaften; Biologie
Pflanzen (Botanik)
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
51941
2020
2020
eng
13
32
postprint
1
2020-05-19
2020-05-19
--
Increasing the affinity of an O-Antigen polysaccharide binding site in Shigella flexneri bacteriophage Sf6 tailspike protein
Broad and unspecific use of antibiotics accelerates spread of resistances. Sensitive and robust pathogen detection is thus important for a more targeted application. Bacteriophages contain a large repertoire of pathogen-binding proteins. These tailspike proteins (TSP) often bind surface glycans and represent a promising design platform for specific pathogen sensors. We analysed bacteriophage Sf6 TSP that recognizes the O-polysaccharide of dysentery-causing Shigella flexneri to develop variants with increased sensitivity for sensor applications. Ligand polyrhamnose backbone conformations were obtained from 2D H-1,H-1-trNOESY NMR utilizing methine-methine and methine-methyl correlations. They agreed well with conformations obtained from molecular dynamics (MD), validating the method for further predictions. In a set of mutants, MD predicted ligand flexibilities that were in good correlation with binding strength as confirmed on immobilized S. flexneri O-polysaccharide (PS) with surface plasmon resonance. In silico approaches combined with rapid screening on PS surfaces hence provide valuable strategies for TSP-based pathogen sensor design.
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
10.25932/publishup-51941
urn:nbn:de:kobv:517-opus4-519418
1866-8372
online registration
publish
<a href="http://publishup.uni-potsdam.de/61417">Bibliographieeintrag der Originalveröffentlichung/Quelle</a>
Chem. Eur. J. 2020, 26, 7263. https://doi.org/10.1002/chem.202000495
Version of Record
false
true
CC-BY-NC - Namensnennung, nicht kommerziell 4.0 International
Ruth Sonja Kunstmann
Olof Engström
Marko Wehle
Göran Widmalm
Mark Santer
Stefanie Barbirz
Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
1417
eng
uncontrolled
carbohydrates
eng
uncontrolled
molecular dynamics simulations
eng
uncontrolled
NMR spectroscopy
eng
uncontrolled
protein-carbohydrate interactions
eng
uncontrolled
surface plasmon resonance
Chemie und zugeordnete Wissenschaften
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Referiert
Green Open-Access
Universität Potsdam
https://publishup.uni-potsdam.de/files/51941/zmnr1417.pdf
62868
2024
2024
2024
eng
133
doctoralthesis
1
--
--
2024-01-30
Chloroplast engineering for recombinant protein production and stress protection
Dissertation, Universität Potsdam, 2024
Lili You
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Universität Potsdam
Universität Potsdam
62867
2024
2024
2024
eng
105
doctoralthesis
1
--
--
2024-02-19
Long-distance circadian coordination via a phloem-delivered mobile transcript
Dissertation, Universität Potsdam, 2024
András Csaba Székely
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Universität Potsdam
Universität Potsdam
62849
2021
2021
eng
12
10
12
article
MDPI
Basel
1
2021-10-01
2021-10-01
--
Coping with environmental extremes
Simple Summary:& nbsp;High alpine meadows are home to numerous endemic butterfly species. A combination of climate change and changes in agricultural practices has led to a severe decline in many species. A seemingly unaffected representative of this habitat is Erebia pronoe. We studied the behaviour, resource use and population structure of this species to explain its resilience and estimate its future survival potential. This species shows pronounced protandry in combination with serial eclosion. Males were significantly more active and mobile and were also caught significantly more often than females, resulting in a pronounced shift in sex ratio in the predicted population structure. The adults use a wide range of nectar plants and establish homeranges in areas of high habitat quality. Thus, Erebia pronoe adults use a wide array of resources combined with a slight specialisation to avoid niche overlap with closely related species. The resulting ecological flexibility seems to be an adaptation to unpredictable environmental conditions, which should be the result of a long-lasting adaptation process. Moreover, the combination of opportunism and modest specialisation should also be a good basis for coping with future changes caused by climate and land-use change.</p> <br /> <br></p> <br /> A mark-recapture study of the nominotypical Erebia pronoe in the Alps was conducted to survey its ecological demands and characteristics. Population structure analysis revealed a combination of protandry (one-week earlier eclosion of males) and serial eclosion. Significant differences between both sexes were found in population density (males: 580/ha & PLUSMN; 37 SE; females: 241/ha & PLUSMN; 66 SE), sex-ratio (2.4) and behaviour (57.7 vs. 11.9% flying). Both sexes used a wide range of nectar plants (Asteraceae, 77.3%; Dipsacaceae, 12.3%; Gentianaceae, 9.7%). The use of nectar plants shows a non-specific spectrum, which, however, completely avoids overlap with the locally co-occurring species Erebia nivalis. Movement patterns show the establishment of homeranges, which significantly limits the migration potential. Due to its broad ecological niche, E. pronoe will probably be able to react plastically to the consequences of climate change. The formation of high population densities, the unconcerned endangerment status, the unspecific resource spectrum and the sedentary character of the species make E. pronoe a potential indicator of the quality and general resource occurrence of alpine rupicolous grasslands.
Insects : open access journal
population ecology and behavioural adaptation of Erebia pronoe, an Alpine butterfly species
10.3390/insects12100896
34680664
2075-4450
outputup:dataSource:PubMed:2021
896
WOS:000711470500001
Wendt, Martin (corresponding author), Senckenberg German Entomol Inst Systemat & Biogeo, Eberswalder Str 90, D-15374 Muncheberg, Germany., martin.wendt@senckenberg.de; n.senftleben@gmail.com; <br /> patrick.gros@hausdernatur.at; Thomas.Schmitt@senckenberg.de
Martin Luther University Halle-Wittenberg
Wendt, Martin
2024-03-01T12:26:01+00:00
sword
importub
filename=package.tar
0fde7af9b07519489490ff6c1b5b5d53
false
true
CC-BY - Namensnennung 4.0 International
Martin Wendt
Nele Senftleben
Patrick Gros
Thomas Schmitt
eng
uncontrolled
mark-release-recapture
eng
uncontrolled
movement patterns
eng
uncontrolled
opportunistic behaviour
eng
uncontrolled
partial protandry
eng
uncontrolled
population demography
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62848
2021
2021
eng
3
11
9
894
article
Elsevier
Amsterdam [u.a.]
1
2021-10-11
2021-10-11
--
Coherent network partitions
We continue to study coherent partitions of graphs whereby the vertex set is partitioned into subsets that induce biclique spanned subgraphs. The problem of identifying the minimum number of edges to obtain biclique spanned connected components (CNP), called the coherence number, is NP-hard even on bipartite graphs. Here, we propose a graph transformation geared towards obtaining an O (log n)-approximation algorithm for the CNP on a bipartite graph with n vertices. The transformation is inspired by a new characterization of biclique spanned subgraphs. In addition, we study coherent partitions on prime graphs, and show that finding coherent partitions reduces to the problem of finding coherent partitions in a prime graph. Therefore, these results provide future directions for approximation algorithms for the coherence number of a given graph.
Theoretical computer science : the journal of the EATCS
Characterizations with cographs and prime graphs
10.1016/j.tcs.2021.10.002
0304-3975
outputup:dataSource:WoS:2021
WOS:000717459300003
Angeleska, Angela (corresponding author), Univ Tampa, Dept Math, 401 W Kennedy Blvd, Tampa, FL 33606 USA., aangeleska@ut.edu; Nikoloski@mpimp-golm.mpg.de
University of Tampa Research Excellence and Scholarly Innovation Award/Dana Foundation Grant
Angeleska, Angela
2024-03-01T11:53:54+00:00
sword
importub
filename=package.tar
4c44f310eb14ec2151c5725d86f9a049
1466347-8
false
true
Angela Angeleska
Sara Omranian
Zoran Nikoloski
eng
uncontrolled
Graph partitions
eng
uncontrolled
Network clustering
eng
uncontrolled
Cographs
eng
uncontrolled
Coherent partition
eng
uncontrolled
Prime graphs
Datenverarbeitung; Informatik
Institut für Biochemie und Biologie
Referiert
Import
62838
2022
2022
eng
12
8
12
article
Wiley
Hoboken
1
2022-07-31
2022-07-31
--
The interaction between metabolic rate, habitat choice, and resource use in a polymorphic freshwater species
Resource polymorphism is common across taxa and can result in alternate ecotypes with specific morphologies, feeding modes, and behaviors that increase performance in a specific habitat. This can result in high intraspecific variation in the expression of specific traits and the extent to which these traits are correlated within a single population. Although metabolic rate influences resource acquisition and the overall pace of life of individuals it is not clear how metabolic rate interacts with the larger suite of traits to ultimately determine individual fitness. We examined the relationship between metabolic rates and the major differences (habitat use, morphology, and resource use) between littoral and pelagic ecotypes of European perch (Perca fluviatilis) from a single lake in Central Sweden. Standard metabolic rate (SMR) was significantly higher in pelagic perch but did not correlate with resource use or morphology. Maximum metabolic rate (MMR) was not correlated with any of our explanatory variables or with SMR. Aerobic scope (AS) showed the same pattern as SMR, differing across habitats, but contrary to expectations, was lower in pelagic perch. This study helps to establish a framework for future experiments further exploring the drivers of intraspecific differences in metabolism. In addition, since metabolic rates scale with temperature and determine predator energy requirements, our observed differences in SMR across habitats will help determine ecotype-specific vulnerabilities to climate change and differences in top-down predation pressure across habitats.
Ecology and evolution
10.1002/ece3.9129
35923943
2045-7758
outputup:dataSource:WoS:2022
e9129
WOS:000833916500001
Eklov, P (corresponding author), Dept Ecol & Genet, Norbyvagen 18d, S-75236 Uppsala, Sweden., peter.eklov@ebc.uu.se
Malmenska studiestiftelsen; Svenska Forskningsradet Formas; [942-2015-365]
Eklöv, Peter
2024-03-01T09:52:16+00:00
sword
importub
filename=package.tar
f9f85e614a9f80244530860531a9b1df
false
true
CC-BY - Namensnennung 4.0 International
Matilda L. Andersson
Kristin Inga Scharnweber
Peter Eklöv
eng
uncontrolled
intraspecific variation
eng
uncontrolled
metabolic rate
eng
uncontrolled
morphometrics
eng
uncontrolled
Perca
eng
uncontrolled
fluviatilis
eng
uncontrolled
plasticity
eng
uncontrolled
resource use
eng
uncontrolled
respirometry
eng
uncontrolled
stable isotopes
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62834
2021
eng
164
171
8
1
8
article
Wiley-VCH
Weinheim
1
2020-12-10
2021-01-04
--
Voltammetry and single-molecule in situ scanning tunnelling microscopy of the redox metalloenzyme human sulfite oxidase
Human sulfite oxidase (hSO) is a homodimeric two-domain enzyme central in the biological sulfur cycle. A pyranopterin molybdenum cofactor (Moco) is the catalytic site and a heme b(5) group located in the N-terminal domain. The two domains are connected by a flexible linker region. Electrons produced at the Moco in sulfite oxidation, are relayed via heme b(5) to electron acceptors or an electrode surface. Inter-domain conformational changes between an open and a closed enzyme conformation, allowing "gated" electron transfer has been suggested. We first recorded cyclic voltammetry (CV) of hSO on single-crystal Au(111)-electrode surfaces modified by self-assembled monolayers (SAMs) both of a short rigid thiol, cysteamine and of a longer structurally flexible thiol, omega-amino-octanethiol (AOT). hSO on cysteamine SAMs displays a well-defined pair of voltammetric peaks around -0.207 V vs. SCE in the absence of sulfite substrate, but no electrocatalysis. hSO on AOT SAMs displays well-defined electrocatalysis, but only "fair" quality voltammetry in the absence of sulfite. We recorded next in situ scanning tunnelling spectroscopy (STS) of hSO on AOT modified Au(111)-electrodes, disclosing, a 2-5 % surface coverage of strong molecular scale contrasts, assigned to single hSO molecules, notably with no contrast difference in the absence and presence of sulfite. In situ STS corroborated this observation with a sigmoidal tunnelling current/overpotential correlation.
ChemElectroChem
10.1002/celc.202001258
2196-0216
outputup:dataSource:WoS:2021
WOS:000607645400021
Ulstrup, Jens (corresponding author), Tech Univ Denmark, Dept Chem, Bldg 207, DK-2800 Lyngby, Denmark., ju@kemi.dtu.dk
Ulstrup, Jens
2024-03-01T08:34:22+00:00
sword
importub
filename=package.tar
b642d161a4ab331302b62203ff30b5ed
false
true
Jiawei Yan
Emil Egede Frøkjær
Christian Engelbrekt
Silke Leimkühler
Jens Ulstrup
Ulla Wollenberger
Xinxin Xiao
Jingdong Zhang
eng
uncontrolled
cyclic voltammetry
eng
uncontrolled
human sulfite oxidase
eng
uncontrolled
in situ scanning
eng
uncontrolled
tunnelling spectroscopy
eng
uncontrolled
self-assembled molecular monolayers
eng
uncontrolled
single-crystal gold electrodes
Chemie und zugeordnete Wissenschaften
Institut für Biochemie und Biologie
Referiert
Import
62821
2021
2021
eng
17
4
11
article
MDPI
Basel
1
2021-02-27
2021-03-27
--
Electrochemical trimethylamine n-oxide biosensor with enzyme-based oxygen-scavenging membrane for long-term operation under ambient air
An amperometric trimethylamine N-oxide (TMAO) biosensor is reported, where TMAO reductase (TorA) and glucose oxidase (GOD) and catalase (Cat) were immobilized on the electrode surface, enabling measurements of mediated enzymatic TMAO reduction at low potential under ambient air conditions. The oxygen anti-interference membrane composed of GOD, Cat and polyvinyl alcohol (PVA) hydrogel, together with glucose concentration, was optimized until the O-2 reduction current of a Clark-type electrode was completely suppressed for at least 3 h. For the preparation of the TMAO biosensor, Escherichia coli TorA was purified under anaerobic conditions and immobilized on the surface of a carbon electrode and covered by the optimized O-2 scavenging membrane. The TMAO sensor operates at a potential of -0.8 V vs. Ag/AgCl (1 M KCl), where the reduction of methylviologen (MV) is recorded. The sensor signal depends linearly on TMAO concentrations between 2 mu M and 15 mM, with a sensitivity of 2.75 +/- 1.7 mu A/mM. The developed biosensor is characterized by a response time of about 33 s and an operational stability over 3 weeks. Furthermore, measurements of TMAO concentration were performed in 10% human serum, where the lowest detectable concentration is of 10 mu M TMAO.
Biosensors : open access journal
10.3390/bios11040098
33801724
2079-6374
outputup:dataSource:WoS:2021
98
WOS:000642801700001
Wollenberger, Ulla (corresponding author), Univ Potsdam, Inst Biochem & Biol, D-14476 Potsdam, Germany., tadjoungwaffo@tu-berlin.de; b.mitrova@gmail.com; <br /> kim.tiedemann@uni-potsdam.de; iobbi@imm.cnrs.fr; sleim@uni-potsdam.de; <br /> uwollen@uni-potsdam.de
Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence StrategyGerman Research Foundation (DFG) [EXC 2008-390540038-UniSysCat]
Wollenberger, Ulla
2024-02-29T12:03:56+00:00
sword
importub
filename=package.tar
ac18f28ae33b2193692c216479287831
false
true
CC-BY - Namensnennung 4.0 International
Armel Franklin Tadjoung Waffo
Biljana Mitrova
Kim Tiedemann
Chantal Iobbi-Nivol
Silke Leimkühler
Ulla Wollenberger
eng
uncontrolled
trimethylamine N-oxide
eng
uncontrolled
biosensor
eng
uncontrolled
TMAO-reductase
eng
uncontrolled
oxygen scavenger
eng
uncontrolled
immobilized enzyme
eng
uncontrolled
multienzyme electrode
eng
uncontrolled
viologen
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
58975
2022
2022
eng
2
5
34
article
Wiley Interscience
New York, NY [u.a.]
1
2022-02-26
2022-02-26
--
Reply to the letter titled: "Pathologizing normal height or identifying chronic malnutrition: Public health concerns of calling stunting normal" / by Nafis Faizi, Mohd Yasir Zubair and Fazeelah Tasleem'. - New York, NY [u.a.] : Wiley Interscience. - 2022. - (American Journal of Human Biology : the Official Journal of the Human Biology Council, 16 Feb 2022. - 34(2022) 5 ). - https://doi.org/10.1002/ajhb.23735
American journal of human biology : the official journal of the Human Biology Association
10.1002/ajhb.23741
35218270
1520-6300
outputup:dataSource:WoS:2022
e23741
WOS:000761226100001
Scheffler, C (corresponding author), Univ Potsdam, Human Biol, Neuen Palais 10, D-14469 Potsdam, Germany., christiane.scheffler@uni-potsdam.de
Scheffler, Christiane
2023-04-24T10:00:08+00:00
sword
importub
filename=package.tar
dc6f347858a2c52f9438e72407eaca49
2001218-4
Christiane Scheffler
Michael Hermanussen
Biowissenschaften; Biologie
Tiere (Zoologie)
Medizin und Gesundheit
Institut für Biochemie und Biologie
Referiert
Import
62809
2022
2022
eng
12
156
article
Elsevier
Oxford
1
2022-08-16
2022-08-16
--
A case for object capabilities as the foundation of a distributed environmental model and simulation infrastructure
With the advent of increasingly powerful computational architectures, scientists use these possibilities to create simulations of ever-increasing size and complexity. Large-scale simulations of environmental systems require huge amounts of resources. Managing these in an operational way becomes increasingly complex and difficult to handle for individual scientists. State-of-the-art simulation infrastructures usually provide the necessary re-sources in a centralised setup, which often results in an all-or-nothing choice for the user. Here, we outline an alternative approach to handling this complexity, while rendering the use of high-performance hardware and large datasets still possible. It retains a number of desirable properties: (i) a decentralised structure, (ii) easy sharing of resources to promote collaboration and (iii) secure access to everything, including natural delegation of authority across levels and system boundaries. We show that the object capability paradigm will cover these issues, and present the first steps towards developing a simulation infrastructure based on these principles.
Environmental modelling & software with environment data news
10.1016/j.envsoft.2022.105471
1364-8152
1873-6726
outputup:dataSource:WoS:2022
105471
WOS:000848653100005
Berg-Mohnicke, M (corresponding author), Leibniz Ctr Agr Landscape Res ZALF, Eberswalder Str 84, D-15374 Muncheberg, Germany., michael.berg-mohnicke@zalf.de
Berg-Mohnicke, Michael
2024-02-28T13:45:37+00:00
sword
importub
filename=package.tar
0bfa876d6d2cc664069711b6ce18b4b5
false
true
CC-BY - Namensnennung 4.0 International
Michael Berg-Mohnicke
Claas Nendel
eng
uncontrolled
Cap'n proto
eng
uncontrolled
Scientific collaboration
eng
uncontrolled
Co -development
eng
uncontrolled
Communication
eng
uncontrolled
protocol
eng
uncontrolled
Object capability
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
62780
2022
2022
eng
801
810
10
67
article
Springer
Dordrecht
1
2022-06-06
2022-06-06
--
A combined de novo assembly approach increases the quality of prokaryotic draft genomes
Next-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes with low contig number and high N50 value can give insight into the structure of the genome as well as provide information on the annotation of the genome. In this study, we designed a pipeline that can be used to assemble prokaryotic draft genomes with low number of contigs and high N50 value. We aimed to use combination of two de novo assembly tools (SPAdes and IDBA-Hybrid) and evaluate the impact of this approach on the quality metrics of the assemblies. The followed pipeline was tested with the raw sequence data with short reads (< 300) for a total of 10 species from four different genera. To obtain the final draft genomes, we firstly assembled the sequences using SPAdes to find closely related organism using the extracted 16 s rRNA from it. IDBA-Hybrid assembler was used to obtain the second assembly data using the closely related organism genome. SPAdes assembler tool was implemented using the second assembly, produced by IDBA-hybrid as a hint. The results were evaluated using QUAST and BUSCO. The pipeline was successful for the reduction of the contig numbers and increasing the N50 statistical values in the draft genome assemblies while preserving the coverage of the draft genomes.
Folia microbiologica : international journal for general, environmental and applied microbiology, and immunology
10.1007/s12223-022-00980-7
35668290
0015-5632
1874-9356
outputup:dataSource:WoS:2022
WOS:000806656300001
Unlu, ES (corresponding author), Abant Izzet Baysal Univ, Fac Arts & Sci, Dept Chem, Bolu, Turkey., esunlu06@gmail.com
Ünlü, Ercan Selçuk
2024-02-26T11:10:58+00:00
sword
importub
filename=package.tar
a3a0b5924182143a84839127a84cd43b
false
true
Uğur Çabuk
Ercan Selçuk Ünlü
eng
uncontrolled
De novo assembly
eng
uncontrolled
Prokaryotes
eng
uncontrolled
Bacteria
eng
uncontrolled
NGS
eng
uncontrolled
Short reads
eng
uncontrolled
Draft genome
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
62749
2022
2022
2022
eng
150
doctoralthesis
1
--
--
2023-09-19
The journey towards the discovery of new protein-metabolite interactions in Arabidopsis thaliana and further functional characterization of selected binding events
Izabela Wojciechowska
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Universität Potsdam
Universität Potsdam
62747
2023
2023
2023
eng
172
doctoralthesis
1
--
--
2023-12-20
Photosynthesis in fluctuating light
Light is the essential energy source for plants to drive photosynthesis. In nature, light availability is highly variable and often fluctuates on very short time scales. As a result, plants developed mechanisms to cope with these fluctuations. Understanding how to improve light use efficiency in natural fluctuating light (FL) conditions is a major target for agronomy.
In the first project, we identified an Arabidopsis thaliana plant that showed reduced levels of rapidly inducible non-photochemical quenching (NPQ). This plant was devoid of any T-DNA insertion. Using a mapping-by-sequencing approach, we successfully located the causal genomic region near the end of chromosome 4. Through variant investigations in that region, we identified a deletion of about 20 kb encompassing 9 genes. By complementation analysis, we confirmed that one of the deleted genes, VTC2, is the causal gene responsible for the low NPQ. Loss of VTC2 decreased NPQ particularly in old leaves, with young leaves being only slightly affected. Additionally, ascorbate levels were almost abolished in old leaves, likely causing the NPQ decrease by reducing the activity of the xanthophyll cycle. Although ascorbate levels in younger leaves were reduced compared to wild-type plants, they remained at a comparably higher level. This difference may be due to the VTC2 paralog VTC5, which is expressed at a higher level in young leaves than in old ones.
Plants require the PROTON GRADIENT REGULATION 5 (PGR5) protein for survival in FL. pgr5 mutants die because they fail to increase the luminal proton concentration in response to high light (HL) phases. A rapid elevation in ∆pH is needed to slow down electron transport through the Cytochrome b6 f complex (photosynthetic control). In FL, such lack of control in the pgr5 mutants results in photosystem I (PSI) overreduction, reactive oxygen species (ROS) production, and cell death. Decreases in photosystem II (PSII) activity introduced by crossing pgr5 with PSII deficient mutants
rescued the lethality of pgr5 in FL. PGR5 was suggested to act as part of the ferredoxin-plastoquinone reductase (FQR), involved in cyclic electron transfer around PSI. However, the proposed molecular role of PGR5 remains highly debated. To learn more about PGR5 function, we performed a forward genetic screen in Arabidopsis thaliana to identify EMS-induced suppressor mutants surviving longer when grown in FL compared to pgr5 mutants (referred to as ”suppressor of pgr5 lethality in fluctuating light”, splf ). 11 different candidate genes were identified in a total of 22 splf plants.
Mutants of seven of these genes in the pgr5 background showed low Fv/Fm values when grown in non-fluctuating low light (LL). Five of these 4genes were previously reported to have a role in PSII biogenesis or function. Two others, RPH1 and a DEAD/DEAH box helicase (AT3G02060), have not been linked to PSII function before. Three of splf candidate genes link to primary metabolism, fructose-2,6-bisphosphatase (F2KP ), udp-glucose pyrophosphorylase 1 (UGP1 ) and ferredoxin-dependent glutamate synthase (Fd-GOGAT ). They are characterized by the fact that they survive longer in FL than pgr5 mutants but do not procede beyond the early vegetative
phase and then die.
Pflanzen wandeln Sonnenlicht durch die Photosynthese in chemische Energie um. In der Natur unterliegt die Verfügbarkeit von Licht jedoch starken Schwankungen, beispielsweise durch kurzzeitige Wolkenverdeckungen. Um mit diesen Veränderungen umzugehen, haben Pflanzen spezielle Mechanismen entwickelt. Das Verständnis, wie die Lichtnutzung unter diesen fluktuierenden Bedingungen optimiert werden kann, stellt eines der Hauptziele in der Landwirtschaft dar. Ziel dieser Arbeit ist es, zu diesem Verständnis beizutragen.
Wir haben eine neue Mutante der Ackerschmalwand identifiziert, die reduzierte Levels des schnell induzierbaren nicht-photochemischen Quenchings (NPQ) aufwies. NPQ ist ein wichtiger Mechanismus, mit dem Pflanzen auf schnelle Wechsel zu stärkerem Licht reagieren können. Die Untersuchung ergab, dass das Fehlen des Gens VTC2 die Ursache für die Reduzierung des NPQ war, mit Auswirkungen auf den Vitamin-C-Spiegel und die Aktivität des Xanthophyllzyklus. Besonders interessant war, dass der Verlust des Gens hauptsächlich ältere Blätter beeinflusste.
Das Gen PGR5 ist für das Überleben von Pflanzen in schwankenden Lichtverhältnissen notwendig. Obwohl viele wissenschaftliche Arbeiten diesem Gen gewidmet sind, sind seine genauen Funktionen nur im Ansatz bekannt. In unserer Studie haben wir Ackerschmalwand Pflanzen ohne dieses Gen mit Chemikalien mutagenisiert und sie dann in schwankenden Lichtverhältnissen wachsen lassen. Dabei konnten wir Suppressormutanten finden, die überlebt haben. Durch diese Herangehensweise haben wir 11 Kandidatengene identifiziert, die eine mögliche Verbindung zum PGR5-Mechanismus aufweisen könnten. Einige dieser Mutanten hemmen das Photosystem II, das für das Einfangen der Lichtenergie verantwortlich ist, während andere Teile den Primärmetabolismus für Zucker und Stickstoff verändern.
Zusammenfassend bietet die Arbeit Einsichten in die Mechanismen, mit denen Pflanzen auf schwankende Lichtbedingungen reagieren, und identifiziert spezifische Gene, die in diesen Prozessen eine Rolle spielen.
pgr5 suppressor mutant screen : low NPQ mutant identification and characterization
Sandrine Kappel
eng
uncontrolled
photosynthesis
eng
uncontrolled
fluctuating light
eng
uncontrolled
PGR5
eng
uncontrolled
suppressor mutant screen
eng
uncontrolled
low NPQ
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Universität Potsdam
Universität Potsdam
62572
2022
2022
eng
15
1
17
article
BMC
London
1
2022-04-28
2022-04-28
--
Insights into the microbiome assembly during different growth stages and storage of strawberry plants
Background: Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches. <br /> Results: Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (10(7)-10(10) marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa. <br /> Conclusion: Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety.
Environmental microbiome
10.1186/s40793-022-00415-3
35484554
2524-6372
outputup:dataSource:WoS:2022
21
WOS:000788582900001
Kusstatscher, P (corresponding author), Graz Univ Technol, Inst Environm Biotechnol, Graz, Austria., peter.kusstatscher@tugraz.at
European Union's Horizon 2020 Research and Innovation Program [81794]
Kusstatscher, Peter
2024-02-07T13:43:02+00:00
sword
importub
filename=package.tar
0b9d4fa74c8af9957b60d9f4ee067603
3007163-X
CC-BY - Namensnennung 4.0 International
Expedito Olimi
Peter Kusstatscher
Wisnu Adi Wicaksono
Ahmed Abdelfattah
Tomislav Cernava
Gabriele Berg
eng
uncontrolled
Fragaria x ananassa
eng
uncontrolled
Microbiome assembly
eng
uncontrolled
Fruit pathogens
eng
uncontrolled
Bacterial
eng
uncontrolled
communities
eng
uncontrolled
Fungal communities
eng
uncontrolled
Amplicon sequencing
eng
uncontrolled
CLSM
Chemie und zugeordnete Wissenschaften
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62719
2021
2020
eng
819
820
2
8
106
article
BMJ Publishing Group
London
1
2021-07-19
2020-07-30
--
Stunting
Archives of disease in childhood : a peer review journal for health professionals and researchers covering conception to adolescence
historical lessons that catch-up growth tells us for mapping growth restoration
10.1136/archdischild-2020-319240
32732317
0003-9888
1468-2044
outputup:dataSource:PubMed:2021
WOS:000678483700029
Rogol, Alan D. (corresponding author), Univ Virginia, Pediat, Charlottesville, VA 22903 USA., adrogol@comcast.net
Rogol, Alan D.
2024-02-22T08:25:24+00:00
sword
importub
filename=package.tar
5b375db7df83c5d7d76b9b87ba345f98
Christiane Scheffler
Michael Hermanussen
Alan D. Rogol
Medizin und Gesundheit
Institut für Biochemie und Biologie
Referiert
Import
Fakultät für Gesundheitswissenschaften
62592
2021
2021
eng
4601
4614
14
19
27
article
Blackwell Science
Oxford [u.a.]
1
2021-07-01
2021-07-01
--
Conservation with elevated elephant densities sequesters carbon in soils despite losses of woody biomass
Nature conservation and restoration in terrestrial ecosystems is often focused on increasing the numbers of megafauna, expecting them to have positive impacts on ecological self-regulation processes and biodiversity. In sub-Saharan Africa, conservation efforts also aspire to protect and enhance biodiversity with particular focus on elephants. However, elephant browsing carries the risk of woody biomass losses. In this context, little is known about how increasing elephant numbers affects carbon stocks in soils, including the subsoils. We hypothesized that (1) increasing numbers of elephants reduce tree biomass, and thus the amount of C stored therein, resulting (2) in a loss of soil organic carbon (SOC). If true, a negative carbon footprint could limit the sustainability of elephant conservation from a global carbon perspective. To test these hypotheses, we selected plots of low, medium, and high elephant densities in two national parks and adjacent conservancies in the Namibian component of the Kavango Zambezi Transfrontier Area (KAZA), and quantified carbon storage in both woody vegetation and soils (1 m). Analyses were supplemented by the assessment of soil carbon isotopic composition. We found that increasing elephant densities resulted in a loss of tree carbon storage by 6.4 t ha(-1). However, and in contrast to our second hypothesis, SOC stocks increased by 4.7 t ha(-1) with increasing elephant densities. These higher SOC stocks were mainly found in the topsoil (0-30 cm) and were largely due to the formation of SOC from woody biomass. A second carbon input source into the soils was megaherbivore dung, which contributed with 0.02-0.323 t C ha(-1) year(-1) to ecosystem carbon storage in the low and high elephant density plots, respectively. Consequently, increasing elephant density does not necessarily lead to a negative C footprint, as soil carbon sequestration and transient C storage in dung almost compensate for losses in tree biomass.
Global change biology
10.1111/gcb.15779
34197679
1354-1013
1365-2486
outputup:dataSource:PubMed:2021
WOS:000673385100001
Sandhage-Hofmann, Alexandra (corresponding author), Univ Bonn, Inst Crop Sci & Resource Conservat Soil Sci & Soi, Nussallee 13, D-53115 Bonn, Germany., sandhage@uni-bonn.de
Deutsche ForschungsgemeinschaftGerman Research Foundation (DFG) [TRR 228/1]
Sandhage-Hofmann, Alexandra
2024-02-08T10:17:01+00:00
sword
importub
filename=package.tar
d73b774f50c621e1a7f297f21d0f9375
2020313-5
1281439-8
false
true
CC-BY-NC - Namensnennung, nicht kommerziell 4.0 International
Alexandra Sandhage-Hofmann
Anja Linstädter
Liana Kindermann
Simon Angombe
Wulf Amelung
eng
uncontrolled
carbon sequestration
eng
uncontrolled
conservation
eng
uncontrolled
elephants
eng
uncontrolled
soil organic carbon
eng
uncontrolled
woody biomass
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
62571
2022
2022
eng
16
6
12
article
MDPI
Basel
1
2022-06-20
2022-06-20
--
First Steps towards the development of epigenetic biomarkers in female cheetahs (Acinonyx jubatus)
Free-ranging cheetahs (Acinonyx jubatus) are generally healthy, whereas cheetahs under human care, such as those in zoological gardens, suffer from ill-defined infectious and degenerative pathologies. These differences are only partially explained by husbandry management programs because both groups share low genetic diversity. However, mounting evidence suggests that physiological differences between populations in different environments can be tracked down to differences in epigenetic signatures. Here, we identified differentially methylated regions (DMRs) between free-ranging cheetahs and conspecifics in zoological gardens and prospect putative links to pathways relevant to immunity, energy balance and homeostasis. Comparing epigenomic DNA methylation profiles obtained from peripheral blood mononuclear cells (PBMCs) from eight free-ranging female cheetahs from Namibia and seven female cheetahs living in zoological gardens within Europe, we identified DMRs of which 22 were hypermethylated and 23 hypomethylated. Hypermethylated regions in cheetahs under human care were located in the promoter region of a gene involved in host-pathogen interactions (KLC1) and in an intron of a transcription factor relevant for the development of pancreatic beta-cells, liver, and kidney (GLIS3). The most canonical mechanism of DNA methylation in promoter regions is assumed to repress gene transcription. Taken together, this could indicate that hypermethylation at the promoter region of KLC1 is involved in the reduced immunity in cheetahs under human care. This approach can be generalized to characterize DNA methylation profiles in larger cheetah populations under human care with a more granular longitudinal data collection, which, in the future, could be used to monitor the early onset of pathologies, and ultimately translate into the development of biomarkers with prophylactic and/or therapeutic potential.
Life : open access journal
10.3390/life12060920
35743950
2075-1729
outputup:dataSource:WoS:2022
920
WOS:000816497900001
Weyrich, A; Fickel, J (corresponding author), Leibniz Inst Zoo & Wildlife Res, Dept Evolutionary Genet, Alfred Kowalke Str 17, D-10315 Berlin, Germany.; Fickel, J (corresponding author), Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24 25, D-14476 Potsdam, Germany.; Wachter, B (corresponding author), Leibniz Inst Zoo & Wildlife Res, Dept Evolutionary Ecol, Alfred Kowalke Str 17, D-10315 Berlin, Germany., weyrich@izw-berlin.de; tania.guerrero@duke.edu; selmayasar94@outlook.de; <br /> czirjak@izw-berlin.de; wachter@izw-berlin.de; fickel@izw-berlin.de
Leibniz Competition Fund [SAW-2018-IZW-3-EpiRank]; Messerli Foundation;; Leibniz Association; Leibniz-IZW
Weyrich, Alexandra
2024-02-07T13:17:47+00:00
sword
importub
filename=package.tar
e5bf6df817f78096d847cb87f78473d2
false
true
CC-BY - Namensnennung 4.0 International
Alexandra Weyrich
Tania P. Guerrero-Altamirano
Selma Yasar
Gábor-Árpád Czirjak
Bettina Wachter
Jörns Fickel
eng
uncontrolled
animals under human care
eng
uncontrolled
captivity
eng
uncontrolled
carnivore
eng
uncontrolled
DNA methylation;
eng
uncontrolled
felidae
eng
uncontrolled
free-ranging
eng
uncontrolled
wildlife
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62694
2022
eng
23
312
article
Elsevier
Amsterdam
1
2021-11-10
2021-11-10
--
Machine learning in crop yield modelling
Provisioning a sufficient stable source of food requires sound knowledge about current and upcoming threats to agricultural production. To that end machine learning approaches were used to identify the prevailing climatic and soil hydrological drivers of spatial and temporal yield variability of four crops, comprising 40 years yield data each from 351 counties in Germany. Effects of progress in agricultural management and breeding were subtracted from the data prior the machine learning modelling by fitting smooth non-linear trends to the 95th percentiles of observed yield data. An extensive feature selection approach was followed then to identify the most relevant predictors out of a large set of candidate predictors, comprising various soil and meteorological data. Particular emphasis was placed on studying the uniqueness of identified key predictors. Random Forest and Support Vector Machine models yielded similar although not identical results, capturing between 50% and 70% of the spatial and temporal variance of silage maize, winter barley, winter rapeseed and winter wheat yield. Equally good performance could be achieved with different sets of predictors. Thus identification of the most reliable models could not be based on the outcome of the model study only but required expert's judgement. Relationships between drivers and response often exhibited optimum curves, especially for summer air temperature and precipitation. In contrast, soil moisture clearly proved less relevant compared to meteorological drivers. In view of the expected climate change both excess precipitation and the excess heat effect deserve more attention in breeding as well as in crop modelling.
Agricultural and forest meteorology
A powerful tool, but no surrogate for science
10.1016/j.agrformet.2021.108698
0168-1923
1873-2240
outputup:dataSource:WoS:2022
108698
WOS:000717364400001
Lischeid, Gunnar (corresponding author), Leibniz Ctr Agr Landscape Res ZALF, Eberswalder Str 84, D-15374 Muncheberg, Germany., lischeid@zalf.de
Lischeid, Gunnar
2024-02-19T10:47:26+00:00
sword
importub
filename=package.tar
97f752ce02e8caa309f5d95f5344ecef
2012165-9
409905-9
false
true
CC-BY-NC-ND - Namensnennung, nicht kommerziell, keine Bearbeitungen 4.0 International
Gunnar Lischeid
Heidi Webber
Michael Sommer
Claas Nendel
Frank Ewert
eng
uncontrolled
Crop modelling
eng
uncontrolled
Machine learning
eng
uncontrolled
Random forests
eng
uncontrolled
Support vector
eng
uncontrolled
machine
eng
uncontrolled
Feature selection
eng
uncontrolled
Equivocality
Geowissenschaften
Landwirtschaft und verwandte Bereiche
Hauswirtschaft und Familie
Institut für Biochemie und Biologie
Referiert
Institut für Umweltwissenschaften und Geographie
Import
Hybrid Open-Access
62707
2023
2023
2024
eng
180, IV
doctoralthesis
1
--
--
2024-02-12
Assessing the genetic architecture underlying systemic responses to variable environments in crops using multi-omics
Plant metabolism serves as the primary mechanism for converting assimilated carbon into essential compounds crucial for plant growth and ultimately, crop yield. This renders it a focal point of research with significant implications. Despite notable strides in comprehending the genetic principles underpinning metabolism and yield, there remains a dearth of knowledge regarding the genetic factors responsible for trait variation under varying environmental conditions. Given the burgeoning global population and the advancing challenges posed by climate change, unraveling the intricacies of metabolic and yield responses to water scarcity became increasingly important in safeguarding food security.
Our research group has recently started to work on the genetic resources of legume species. To this end, the study presented here investigates the metabolic diversity across five different legume species at a tissue level, identifying species-specific biosynthesis of alkaloids as well as iso-/flavonoids with diverse functional groups, namely prenylation, phenylacylation as well as methoxylation, to create a resource for follow up studies investigation the metabolic diversity in natural diverse populations of legume species.
Following this, the second study investigates the genetic architecture of drought-induced changes in a global common bean population. Here, a plethora of quantitative trait loci (QTL) associated with various traits are identified by performing genome-wide association studies (GWAS), including for lipid signaling. On this site, overexpression of candidates highlighted the induction of several oxylipins reported to be pivotal in coping with harsh environmental conditions such as water scarcity.
Diverging from the common bean and GWAS, the following study focuses on identifying drought-related QTL in tomato using a bi-parental breeding population. This descriptive study highlights novel multi-omic QTL, including metabolism, photosynthesis as well as fruit setting, some of which are uniquely assigned under drought. Compared to conventional approaches using the bi-parental IL population, the study presented improves the resolution by assessing further backcrossed ILs, named sub-ILs.
In the final study, a photosynthetic gene, namely a PetM subunit of the cytochrome b6f complex encoding gene, involved in electron flow is characterized in an horticultural important crop. While several advances have been made in model organisms, this study highlights the transition of this fundamental knowledge to horticultural important crops, such as tomato, and investigates its function under differing light conditions. Overall, the presented thesis combines different strategies in unveiling the genetic components in multi-omic traits under drought using conventional breeding populations as well as a diverse global population. To this end, it allows a comparison of either approach and highlights their strengths and weaknesses.
Der pflanzliche Stoffwechsel ist der wichtigste Mechanismus für die Umwandlung von assimiliertem Kohlenstoff in essenzielle Verbindungen, die für das Pflanzenwachstum und letztlich den Ernteertrag entscheidend sind. Dies macht ihn zu einem Schwerpunkt der Forschung mit erheblichen Auswirkungen. Trotz bemerkenswerter Fortschritte beim Verständnis der genetischen Prinzipien, die dem Stoffwechsel und den Erträgen zugrunde liegen, gibt es nach wie vor einen Mangel an Wissen über die genetischen Faktoren, die für die Variation von Merkmalen unter verschiedenen Umweltbedingungen verantwortlich sind. In Anbetracht der wachsenden Weltbevölkerung und der zunehmenden Herausforderungen durch den Klimawandel wird es immer wichtiger, die Feinheiten des Stoffwechsels und des Ertrags auf Wasserknappheit zu entschlüsseln, um die Ernährungssicherheit zu gewährleisten.
Unsere Forschungsgruppe hat vor kurzem damit begonnen, sich mit den genetischen Ressourcen von Leguminosen zu befassen. Zu diesem Zweck untersucht die hier vorgestellte Studie die Stoffwechselvielfalt bei fünf verschiedenen Leguminosen auf Gewebeebene und identifiziert die artspezifische Biosynthese von Alkaloiden sowie Iso-/Flavonoiden mit verschiedenen funktionellen Gruppen, nämlich Prenylierung, Phenylacylierung sowie Methoxylierung, um eine Ressource für Folgestudien zu schaffen, die die Stoffwechselvielfalt in verschiedenen natürlichen Populationen von Leguminosen untersuchen.
Im Anschluss daran wird in der zweiten Studie die genetische Architektur trockenheitsbedingter Veränderungen in einer globalen Bohnenpopulation untersucht. Hier wird eine Vielzahl von quantitativen Merkmalsloci (QTL) identifiziert, die mit verschiedenen Merkmalen assoziiert sind, darunter auch für die Lipidsignalübertragung, unter Durchführung genomweite Assoziationsstudien (GWAS). Die Überexpression von Kandidaten auf dieser Seite hat die Induktion mehrerer Oxylipine hervorgehoben, die Berichten zufolge für die Bewältigung rauer Umweltbedingungen wie Wasserknappheit von zentraler Bedeutung sind.
Abweichend von der Bohne und der GWAS konzentriert sich die folgende Studie auf die Identifizierung trockenheitsbezogener QTL bei der Tomate unter Verwendung einer bi-elterlichen Zuchtpopulation. Diese deskriptive Studie hebt neuartige multi-omische QTL hervor, einschließlich für Stoffwechsel, Photosynthese und Fruchtansatz, von denen einige eindeutig dem Dürre-Stress zugeordnet werden. Im Vergleich zu herkömmlichen Ansätzen, bei denen die bi-elterliche IL-Population verwendet wird, verbessert die vorgestellte Studie die Auflösung, indem weitere rückgekreuzte ILs, so genannte sub-ILs, untersucht werden.
In der letzten Studie wird ein photosynthetisches Gen, nämlich eine PetM-Untereinheit des Cytochrom b6fKomplexes, das am Elektronenfluss beteiligt ist, in einer für den Gartenbau wichtigen Pflanze charakterisiert. Während bei Modellorganismen bereits zahlreiche wissenschaftliche Fortschritte erzielt wurden, beleuchtet diese Studie den Übergang dieses grundlegenden Wissens auf wichtige Gartenbaupflanzen wie die Tomate und untersucht ihre Funktion unter verschiedenen Lichtbedingungen.
Insgesamt werden in der vorliegenden Arbeit verschiedene Strategien kombiniert, um die genetischen Komponenten multi-omischer Merkmale bei Trockenheit aufzudecken, wobei sowohl konventionelle Zuchtpopulationen als auch eine vielfältige globale Population verwendet werden. Zu diesem Zweck ermöglicht sie einen Vergleich beider Ansätze und zeigt ihre Stärken und Schwächen auf.
Dissertation, Universität Potsdam, 2024
Mustafa Bulut
eng
uncontrolled
genomics
eng
uncontrolled
metabolomics
eng
uncontrolled
phenomics
eng
uncontrolled
genome-wide association studies (GWAS)
eng
uncontrolled
genotype-by-Environmental interaction (GxE)
eng
uncontrolled
plasticity
Pflanzen (Botanik)
Institut für Biochemie und Biologie
Universität Potsdam
Universität Potsdam
62656
2022
2022
eng
3177
3186
10
10
414
article
Springer
Heidelberg
1
2022-01-19
2022-01-19
--
Lateral flow-based nucleic acid detection of SARS-CoV-2 using enzymatic incorporation of biotin-labeled dUTP for POCT use
The degree of detrimental effects inflicted on mankind by the COVID-19 pandemic increased the need to develop ASSURED (Affordable, Sensitive, Specific, User-friendly, Rapid and Robust, Equipment-free, and Deliverable) POCT (point of care testing) to overcome the current and any future pandemics. Much effort in research and development is currently advancing the progress to overcome the diagnostic pressure built up by emerging new pathogens. LAMP (loop-mediated isothermal amplification) is a well-researched isothermal technique for specific nucleic acid amplification which can be combined with a highly sensitive immunochromatographic readout via lateral flow assays (LFA). Here we discuss LAMP-LFA robustness, sensitivity, and specificity for SARS-CoV-2 N-gene detection in cDNA and clinical swab-extracted RNA samples. The LFA readout is designed to produce highly specific results by incorporation of biotin and FITC labels to 11-dUTP and LF (loop forming forward) primer, respectively. The LAMP-LFA assay was established using cDNA for N-gene with an accuracy of 95.65%. To validate the study, 82 SARS-CoV-2-positive RNA samples were tested. Reverse transcriptase (RT)-LAMP-LFA was positive for the RNA samples with an accuracy of 81.66%; SARS-CoV-2 viral RNA was detected by RT-LAMP-LFA for as low as CT-33. Our method reduced the detection time to 15 min and indicates therefore that RT-LAMP in combination with LFA represents a promising nucleic acid biosensing POCT platform that combines with smartphone based semi-quantitative data analysis.
Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica
10.1007/s00216-022-03880-4
35044487
1618-2642
1618-2650
outputup:dataSource:WoS:2022
WOS:000744405000003
Bier, FF (corresponding author), Univ Potsdam, Inst Biochem & Biol, Chair Mol Bioanal & Bioelect, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany.; Bier, FF (corresponding author), Inst Mol Diagnost & Bioanal IMDB gGmbH, Veltener Str 12, D-16761 Hennigsdorf, Germany., agarwal@uni-potsdam.de; christian.Warmt@izi-bb.fraunhofer.de; <br /> joerg.henkel@izi-bb.fraunhofer.de; SchrickL@rki.de; NitscheA@rki.de; <br /> fbier@uni-potsdam.de
BMBF (Federal Ministry of Education and Research, Germany) [03COV22A/B];; Projekt DEAL
Bier, Frank F.
2024-02-15T12:06:52+00:00
sword
importub
filename=package.tar
cc28c32d0721672acf123314cafa1956
2071767-2
CC-BY - Namensnennung 4.0 International
Saloni Agarwal
Christian Warmt
Jörg Henkel
Livia Schrick
Andreas Nitsche
Frank Fabian Bier
eng
uncontrolled
Point of care testing (POCT)
eng
uncontrolled
Lateral flow assay (LFA)
eng
uncontrolled
COVID-19
eng
uncontrolled
Reverse transcription loop-mediated isothermal amplification (RT-LAMP);
eng
uncontrolled
SARS-CoV-2 N-gene
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
62657
2022
2022
eng
8
article
Wiley-VCH
Weinheim
1
2022-06-05
2022-06-05
--
Infrared spectroscopy flucidates the inhibitor binding sites in a metal-dependent formate dehydrogenase
Biological carbon dioxide (CO2) reduction is an important step by which organisms form valuable energy-richer molecules required for further metabolic processes. The Mo-dependent formate dehydrogenase (FDH) from Rhodobacter capsulatus catalyzes reversible formate oxidation to CO2 at a bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor. To elucidate potential substrate binding sites relevant for the mechanism, we studied herein the interaction with the inhibitory molecules azide and cyanate, which are isoelectronic to CO2 and charged as formate. We employed infrared (IR) spectroscopy in combination with density functional theory (DFT) and inhibition kinetics. One distinct inhibitory molecule was found to bind to either a non-competitive or a competitive binding site in the secondary coordination sphere of the active site. Site-directed mutagenesis of key amino acid residues in the vicinity of the bis-MGD cofactor revealed changes in both non-competitive and competitive binding, whereby the inhibitor is in case of the latter interaction presumably bound between the cofactor and the adjacent Arg587.
Chemistry - a European journal
10.1002/chem.202201091
35662280
0947-6539
1521-3765
outputup:dataSource:WoS:2022
e202201091
WOS:000835372300001
Mroginski, MA; Zebger, I (corresponding author), Tech Univ Berlin, Inst Chem, Max Volmer Lab Biophys Chem, PC14,Str 17 Juni 135, D-10623 Berlin, Germany.; Leimkuhler, S (corresponding author), Univ Potsdam, Inst Biochem & Biol, Mol Enzymol, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany., andrea.mroginski@tu-berlin.de; sleim@uni-potsdam.de; <br /> ingo.zebger@tu-berlin.de
DFG [EXC 2008/1-390540038]; Einstein Foundation Berlin (Einstein Center; of Catalysis); BIG-NSE; EU [810856]; Projekt DEAL
Leimkühler, Silke
2024-02-15T12:38:55+00:00
sword
importub
filename=package.tar
dca463b4b7b21da4be35f60dc12e7bf7
1478547-X
false
true
CC-BY - Namensnennung 4.0 International
Konstantin Laun
Benjamin R. Duffus
Stefan Wahlefeld
Sagie Katz
Dennis Heinz Belger
Peter Hildebrandt
Maria Andrea Mroginski
Silke Leimkühler
Ingo Zebger
eng
uncontrolled
CO2 reduction
eng
uncontrolled
DFT
eng
uncontrolled
formate oxidation
eng
uncontrolled
inhibition kinetics
eng
uncontrolled
IR
eng
uncontrolled
spectroscopy
eng
uncontrolled
molybdoenzyme
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
61106
2020
2020
eng
21
9
article
eLife Sciences Publications
Cambridge
1
2020-05-22
2020-05-22
--
Identification of a super-functional Tfh-like subpopulation in murine lupus by pattern perception
Dysregulated cytokine expression by T cells plays a pivotal role in the pathogenesis of autoimmune diseases. However, the identification of the corresponding pathogenic subpopulations is a challenge, since a distinction between physiological variation and a new quality in the expression of protein markers requires combinatorial evaluation. Here, we were able to identify a super-functional follicular helper T cell (Tfh)-like subpopulation in lupus-prone NZBxW mice with our binning approach "pattern recognition of immune cells (PRI)". PRI uncovered a subpopulation of IL-21(+) IFN-gamma(high) PD-1(low) CD40L(high) CXCR5(-) Bcl-6(-) T cells specifically expanded in diseased mice. In addition, these cells express high levels of TNF-alpha and IL-2, and provide B cell help for IgG production in an IL-21 and CD40L dependent manner. This super-functional T cell subset might be a superior driver of autoimmune processes due to a polyfunctional and high cytokine expression combined with Tfh-like properties.
eLife
10.7554/eLife.53226
32441253
2050-084X
outputup:dataSource:Crossref:2020
e53226
WOS:000538567800001
Gryzik, S; Hoang, Y; Mohr, E; Baumgrass, R (corresponding author), German Rheumatism Res Ctr DRFZ, Berlin, Germany.; Hoang, Y; Baumgrass, R (corresponding author), Univ Potsdam, Potsdam, Germany., s_gryzik@web.de; yen.hoang@drfz.de; elodie.mohr@drfz.de; <br /> baumgrass@drfz.de
Bundesministerium fur Bildung und ForschungFederal Ministry of Education; & Research (BMBF) [0316164A]
Gryzik, Stefanie
Hoang, Yen
Mohr, Elodie
Baumgrass, Ria
2023-10-20T06:21:17+00:00
sword
importub
filename=package.tar
7a65d2b9be70a36101066e559f929e1f
2687154-3
false
true
CC-BY - Namensnennung 4.0 International
Stefanie Gryzik
Yen Hoang
Timo Lischke
Elodie Mohr
Melanie Venzke
Isabelle Kadner
Josephine Pötzsch
Detlef Groth
Andreas Radbruch
Andreas Hutloff
Ria Baumgrass
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62457
2022
2022
eng
3881
3897
17
12
73
article
Oxford Univ. Press
Oxford
1
2022-04-16
2022-04-16
--
Phytochrome-interacting factors
Review exploring the regulation of PHYTOCHROME-INTERACTING FACTORS by light, their role in abiotic stress tolerance and plant architecture, and their influence on crop productivity.
Light is a key determinant for plant growth, development, and ultimately yield. Phytochromes, red/far-red photoreceptors, play an important role in plant architecture, stress tolerance, and productivity. In the model plant Arabidopsis, it has been shown that PHYTOCHROME-INTERACTING FACTORS (PIFs; bHLH transcription factors) act as central hubs in the integration of external stimuli to regulate plant development. Recent studies have unveiled the importance of PIFs in crops. They are involved in the modulation of plant architecture and productivity through the regulation of cell division and elongation in response to different environmental cues. These studies show that different PIFs have overlapping but also distinct functions in the regulation of plant growth. Therefore, understanding the molecular mechanisms by which PIFs regulate plant development is crucial to improve crop productivity under both optimal and adverse environmental conditions. In this review, we discuss current knowledge of PIFs acting as integrators of light and other signals in different crops, with particular focus on the role of PIFs in responding to different environmental conditions and how this can be used to improve crop productivity.
Journal of experimental botany
a promising tool to improve crop productivity
10.1093/jxb/erac142
35429385
0022-0957
1460-2431
outputup:dataSource:WoS:2022
WOS:000810101200001
Saibo, NJM (corresponding author), Univ Nova Lisboa, Inst Tecnol Quim & Biol Antonio Xavier, Av Republ, P-2780157 Oeiras, Portugal., saibo@itqb.unl.pt
Fundacao para a Ciencia e Tecnologia (FCT) [PTDC/BIA-FBT/31070/2017,; UI/BD/151210/2021, PD/BD/114416/2016]; Fundacao para a Ciencia e; Tecnologia (FCT) through GREEN-IT Bioresources for Sustainability RD; Unit [UIDB/04551/2020, UIDP/04551/2020]
Saibo, Nelson J. M.
2024-02-02T09:13:26+00:00
sword
importub
filename=package.tar
e7d478e4d511b8faf1fdc1a9a6dade97
1466717-4
2976-2
Andre M. Cordeiro
Luis Andrade
Catarina C. Monteiro
Guilherme Leitao
Philip Anthony Wigge
Nelson J. M. Saibo
eng
uncontrolled
Cold
eng
uncontrolled
drought
eng
uncontrolled
grain size
eng
uncontrolled
heat
eng
uncontrolled
light signaling
eng
uncontrolled
phytochrome
eng
uncontrolled
PIF
eng
uncontrolled
plant architecture
eng
uncontrolled
plant breeding
eng
uncontrolled
plant yield
eng
uncontrolled
salinity
Pflanzen (Botanik)
Institut für Biochemie und Biologie
Referiert
Import
62448
2022
2022
eng
1857
1867
11
4
14
article
Copernicus
Göttingen
1
2022-04-19
2022-04-19
--
Spatial and seasonal patterns of water isotopes in northeastern German lakes
Water stable isotopes (delta O-18 and delta H-2) were analyzed in samples collected in lakes, associated with riverine systems in northeastern Germany, throughout 2020. The dataset (Aichner et al., 2021; https://doi.org/10.1594/PANGAEA.935633) is derived from water samples collected at (a) lake shores (sampled in March and July 2020), (b) buoys which were temporarily installed in deep parts of the lake (sampled monthly from March to October 2020), (c) multiple spatially distributed spots in four selected lakes (in September 2020), and (d) the outflow of Muggelsee (sampled biweekly from March 2020 to January 2021). At shores, water was sampled with a pipette from 40-60 cm below the water surface and directly transferred into a measurement vial, while at buoys a Limnos water sampler was used to obtain samples from 1 m below the surface. Isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer, with a measurement uncertainty of < 0.15 parts per thousand (delta O-18) and < 0.0 parts per thousand (delta H-2). The data give information about the vegetation period and the full seasonal isotope amplitude in the sampled lakes and about spatial isotope variability in different branches of the associated riverine systems.
Earth system science data : ESSD
10.5194/essd-14-1857-2022
1866-3508
1866-3516
outputup:dataSource:WoS:2022
WOS:000783503300001
Aichner, B (corresponding author), Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Community & Ecosyst Ecol 2, Muggelseedamm 301, Berlin, Germany., bernhard.aichner@gmx.de
Deutsche Forschungsgemeinschaft [Ai 134/3-1]; Leibniz Association; [K45/2017]
Aichner, Bernhard
2024-02-02T07:29:15+00:00
sword
importub
filename=package.tar
137c9c901e62d93617d5bd9d2b04dbc0
2475469-9
2442009-8
false
true
CC-BY - Namensnennung 4.0 International
Bernhard Aichner
David Dubbert
Christine Kiel
Katrin Kohnert
Igor Ogashawara
Andreas Jechow
Sarah-Faye Harpenslager
Franz Hölker
Jens Christian Nejstgaard
Hans-Peter Grossart
Gabriel Singer
Sabine Wollrab
Stella Angela Berger
Geowissenschaften
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62433
2022
2022
eng
1920
1933
14
article
Wiley
Hoboken
1
2022-07-29
2022-07-29
--
Activity of AC electrokinetically immobilized horseradish peroxidase
Dielectrophoresis (DEP) is an AC electrokinetic effect mainly used to manipulate cells. Smaller particles, like virions, antibodies, enzymes, and even dye molecules can be immobilized by DEP as well. In principle, it was shown that enzymes are active after immobilization by DEP, but no quantification of the retained activity was reported so far. In this study, the activity of the enzyme horseradish peroxidase (HRP) is quantified after immobilization by DEP. For this, HRP is immobilized on regular arrays of titanium nitride ring electrodes of 500 nm diameter and 20 nm widths. The activity of HRP on the electrode chip is measured with a limit of detection of 60 fg HRP by observing the enzymatic turnover of Amplex Red and H2O2 to fluorescent resorufin by fluorescence microscopy. The initial activity of the permanently immobilized HRP equals up to 45% of the activity that can be expected for an ideal monolayer of HRP molecules on all electrodes of the array. Localization of the immobilizate on the electrodes is accomplished by staining with the fluorescent product of the enzyme reaction. The high residual activity of enzymes after AC field induced immobilization shows the method's suitability for biosensing and research applications.
Electrophoresis : microfluidics, nanoanalysis & proteomics
10.1002/elps.202200073
35904497
0173-0835
1522-2683
outputup:dataSource:WoS:2022
WOS:000837814800001
Prufer, M (corresponding author), Fraunhofer Inst Cell Therapy & Immunol, Branch Bioanalyt & Bioproc IZI BB, Muhlenberg 13, D-14476 Potsdam, Germany., Mareike.Pruefer@izi-bb.fraunhofer.de
European Regional Development Fund (ERDF); Brandenburg Ministry of; Science, Research and Cultural Affairs (MWFK)
Hölzel, Ralph
2024-02-01T16:28:33+00:00
sword
importub
filename=package.tar
dff54e1009b4cf7885642b418aa0dbb3
1475486-1
619001-7
false
true
CC-BY - Namensnennung 4.0 International
Mareike Prüfer
Christian Wenger
Frank Fabian Bier
Eva-Maria Laux
Ralph Hölzel
eng
uncontrolled
AC electrokinetics
eng
uncontrolled
dielectrophoresis
eng
uncontrolled
enzyme activity
eng
uncontrolled
immobilization;
eng
uncontrolled
nanoelectrodes
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
62430
2022
2022
eng
646
648
3
4
7
article
Routledge, Taylor & Francis Group
Abingdon
1
2022-04-14
2022-04-14
--
Mitochondrial genomes of the freshwater monogonont rotifer Brachionus fernandoi and of two additional B. calyciflorus sensu stricto lineages from Germany and the USA (Rotifera, Brachionidae)
The Brachionus calyciflorus species complex was recently subdivided into four species, but genetic resources to resolve phylogenetic relationships within this complex are still lacking. We provide two complete mitochondrial (mt) genomes from B. calyciflorus sensu stricto (Germany, USA) and the mt coding sequences (cds) from a German B. fernandoi. Phylogenetic analysis placed our B. calyciflorus sensu stricto strains close to the published genomes of B. calyciflorus, forming the putative sister species to B. fernandoi. Global representatives of B. calyciflorus sensu stricto (i.e. Europe, USA, and China) are genetically closer related to each other than to B. fernandoi (average pairwise nucleotide diversity 0.079 intraspecific vs. 0.254 interspecific).
Mitochondrial DNA. Part B-Resources
10.1080/23802359.2022.2060765
35478860
2380-2359
outputup:dataSource:WoS:2022
WOS:000782921700001
Tiedemann, R (corresponding author), Univ Potsdam, Inst Biochem & Biol, Unit Evolutionary Biol Systemat Zool, Potsdam, Germany., tiedeman@uni-potsdam.de
Deutsche Forschungsgemeinschaft (DFG) [DFG-GRK 2118]
Tiedemann, Ralph
2024-02-01T14:11:07+00:00
sword
importub
filename=package.tar
841a735efb93b06e6d1e6f3398790cde
2868557-X
CC-BY - Namensnennung 4.0 International
Katrin Kiemel
Binia De Cahsan
Sofia Paraskevopoulou
Guntram Weithoff
Ralph Tiedemann
eng
uncontrolled
Mitogenome
eng
uncontrolled
cryptic species
eng
uncontrolled
Brachionus calyciflorus s
eng
uncontrolled
Brachionus
eng
uncontrolled
fernandoi
eng
uncontrolled
monogonont rotifer
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62407
2022
2022
eng
7
1
3
article
Wiley
Hoboken
1
2022-02-01
2022-02-01
--
Transition zones across agricultural field boundaries for integrated landscape research and management of biodiversity and yields
Biodiversity conservation and agricultural production have been largely framed as separate goals for landscapes in the discourse on land use. Although there is an increasing tendency to move away from this dichotomy in theory, the tendency is perpetuated by the spatially explicit approaches used in research and management practice. Transition zones (TZ) have previously been defined as areas where two adjacent fields or patches interact, and so they occur abundantly throughout agricultural landscapes. Biodiversity patterns in TZ have been extensively studied, but their relationship to yield patterns and social-ecological dimensions has been largely neglected. Focusing on European, temperate agricultural landscapes, we outline three areas of research and management that together demonstrate how TZ might be used to facilitate an integrated landscape approach: (i) plant and animal species' use and response to boundaries and the resulting effects on yield, for a deeper understanding of how landscape structure shapes quantity and quality of TZ; (ii) local knowledge on field or patch-level management and its interactions with biodiversity and yield in TZ, and (iii) conflict prevention and collaborative management across land-use boundaries.
Ecological solutions and evidence
10.1002/2688-8319.12122
2688-8319
outputup:dataSource:WoS:2022
e12122
WOS:000794141100005
Kernecker, M (corresponding author), Leibniz Ctr Agr Landscape Res, Eberswalder Str 84, D-15374 Muncheberg, Germany., maria.kernecker@zalf.de
Deutsche Forschungsgemeinschaft [420434427]; Bundesministerium fur; Bildung und Forschung [01LC1406A-E, 031B0751]
Kernecker, Maria
2024-02-01T07:21:40+00:00
sword
importub
filename=package.tar
d90a576cc179708c1334857606ae7944
3021448-8
false
true
CC-BY - Namensnennung 4.0 International
Maria Kernecker
Meike Fienitz
Claas Nendel
Marlene Paetzig
Karin Pirhofer Walzl
Larissa Raatz
Martin Schmidt
Monika Wulf
Jana Zscheischler
eng
uncontrolled
ecotones
eng
uncontrolled
field boundaries
eng
uncontrolled
functional traits
eng
uncontrolled
landscape complexity;
eng
uncontrolled
land-use conflicts
eng
uncontrolled
local knowledge
eng
uncontrolled
spillovers
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62404
2022
2022
eng
20
1
20
article
BMC
London
1
2022-02-21
2022-02-21
--
Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits
Background
Long-term selection experiments are a powerful tool to understand the genetic background of complex traits. The longest of such experiments has been conducted in the Research Institute for Farm Animal Biology (FBN), generating extreme mouse lines with increased fertility, body mass, protein mass and endurance. For >140 generations, these lines have been maintained alongside an unselected control line, representing a valuable resource for understanding the genetic basis of polygenic traits. However, their history and genomes have not been reported in a comprehensive manner yet. Therefore, the aim of this study is to provide a summary of the breeding history and phenotypic traits of these lines along with their genomic characteristics. We further attempt to decipher the effects of the observed line-specific patterns of genetic variation on each of the selected traits.
Results
Over the course of >140 generations, selection on the control line has given rise to two extremely fertile lines (>20 pups per litter each), two giant growth lines (one lean, one obese) and one long-distance running line. Whole genome sequencing analysis on 25 animals per line revealed line-specific patterns of genetic variation among lines, as well as high levels of homozygosity within lines. This high degree of distinctiveness results from the combined effects of long-term continuous selection, genetic drift, population bottleneck and isolation. Detection of line-specific patterns of genetic differentiation and structural variation revealed multiple candidate genes behind the improvement of the selected traits.
Conclusions
The genomes of the Dummerstorf trait-selected mouse lines display distinct patterns of genomic variation harbouring multiple trait-relevant genes. Low levels of within-line genetic diversity indicate that many of the beneficial alleles have arrived to fixation alongside with neutral alleles. This study represents the first step in deciphering the influence of selection and neutral evolutionary forces on the genomes of these extreme mouse lines and depicts the genetic complexity underlying polygenic traits.
BMC Biology
10.1186/s12915-022-01248-9
35189878
1741-7007
outputup:dataSource:WoS:2022
52
WOS:000758815800001
Palma-Vera, SE (corresponding author), Res Inst Farm Anim Biol FBN, Inst Reprod Biol, Dummerstorf, Germany., serpalma.v@gmail.com
Leibniz Collaborative Excellence programme [K52/2017]; DFG [407495230,; 423957469]; Projekt DEAL
Palma-Vera, Sergio E.
2024-02-01T06:40:07+00:00
sword
importub
filename=package.tar
31db25f0b2e60bb72d35ea0b0989e276
2133020-7
false
true
CC-BY - Namensnennung 4.0 International
Sergio E. Palma-Vera
Henry Reyer
Martina Langhammer
Norbert Reinsch
Lorena Derezanin
Jörns Fickel
Saber Qanbari
Joachim M. Weitzel
Soeren Franzenburg
Georg Hemmrich-Stanisak
Jennifer Schön
eng
uncontrolled
Mouse
eng
uncontrolled
Fertility
eng
uncontrolled
Body mass
eng
uncontrolled
Endurance
eng
uncontrolled
Selective breeding
eng
uncontrolled
Genetic
eng
uncontrolled
drift
eng
uncontrolled
Bottleneck
eng
uncontrolled
Whole genome sequencing
eng
uncontrolled
Single-nucleotide
eng
uncontrolled
polymorphism
eng
uncontrolled
Structural variation
Biowissenschaften; Biologie
Medizin und Gesundheit
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
61537
2022
2022
eng
8
318
review
Elsevier Science
Amsterdam [u.a.]
1
2022-05-01
2022-05-01
--
A review of starch, a unique biopolymer - structure, metabolism and in planta modifications
Starch is a complex carbohydrate polymer produced by plants and especially by crops in huge amounts. It consists of amylose and amylopectin, which have alpha-1,4-and alpha-1,6-linked glucose units. Despite this simple chemistry, the entire starch metabolism is complex, containing various (iso)enzymes/proteins. However, whose interplay is still not yet fully understood. Starch is essential for humans and animals as a source of nutrition and energy. Nowadays, starch is also commonly used in non-food industrial sectors for a variety of purposes. However, native starches do not always satisfy the needs of a wide range of (industrial) applications. This review summarizes the structural properties of starch, analytical methods for starch characterization, and in planta starch modifications.
Plant science : an international journal of experimental plant biology
10.1016/j.plantsci.2022.111223
35351303
0168-9452
1873-2259
outputup:dataSource:WoS:2022
111223
WOS:000779424100006
Fettke, J (corresponding author), Univ Potsdam, Inst Biochem & Biol, Biopolymer Analyt, Karl Liebknecht Str 24-25,Bldg 20, D-14476 Potsdam, Germany., fettke@uni-potsdam.de
Deutsche Forschungsgemeinschaft DFG [DFG-FE1030/5-1, FE1030/6-1]
Fettke, Joerg
2023-11-23T11:21:03+00:00
sword
importub
filename=package.tar
6b19021e373427630584b3f2483dafdb
1498605-X
742010-9
false
true
CC-BY-NC-ND - Namensnennung, nicht kommerziell, keine Bearbeitungen 4.0 International
Ardha Apriyanto
Julia Compart
Jörg Fettke
eng
uncontrolled
starch
eng
uncontrolled
starch structure
eng
uncontrolled
starch surface
eng
uncontrolled
starch modifications;
eng
uncontrolled
analytics
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
62383
2019
2019
deu
46
47
2
article
oerding print GmbH
Braunschweig
1
--
--
--
Warum hat Bayern mehr Feldhasen als Brandenburg?
Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
false
true
Ullmann Wiebke
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
62385
2019
2019
deu
54
55
2
article
oerding print GmbH
Braunschweig
1
--
--
--
Gefahr an jeder Ecke
Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
wie die Landschaftsstruktur die Verteilung von Beutetieren beeinflusst
false
true
Lisa Teckentrup
Pflanzen (Botanik)
Institut für Biochemie und Biologie
62384
2019
2019
deu
52
53
2
article
oerding print GmbH
Braunschweig
1
--
--
--
Mut macht einsam
Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
der Einfluss von Persönlichkeit auf das Zusammenleben von Tieren
false
true
Merlin Schäfer
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
62382
2019
2019
deu
41
42
2
article
oerding print GmbH
Braunschweig
1
--
--
--
Auf dem Sprung
Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
wie bewegen sich Tiere durch die Landschaft?
false
true
Gabriele Joanna Kowalski
Tiere (Zoologie)
Institut für Biochemie und Biologie
62381
2019
2019
deu
32
33
2
article
oerding print GmbH
Braunschweig
1
--
--
--
Wirtschaften in einer reich strukturierten Landschaft - geht das ?
Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
false
true
Larissa Raatz
Geowissenschaften
Institut für Biochemie und Biologie
62380
2019
2019
deu
30
31
2
article
oerding print GmbH
Braunschweig
1
--
--
--
Können auch Pflanzen zwischen den Söllen "wandern"
Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
false
true
Sissi Donna Lozada Gobilard
Pflanzen (Botanik)
Institut für Biochemie und Biologie
62379
2019
2019
deu
28
29
2
article
oerding print GmbH
Braunschweig
1
--
--
--
Wie und wohin reisen Wasserflöhe?
Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
Magdalena Litwin
Pierluigi Colangeli
Tiere (Zoologie)
Institut für Biochemie und Biologie
62378
2019
2019
deu
24
25
2
article
oerding print GmbH
Braunschweig
1
--
--
--
Blick in die Zukunft
Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
wie werden sich Pflanzengemeinschaften in Brandenburg verändern?
false
true
Stefanie Maaß
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
62377
2019
2019
deu
20
21
2
article
oerding print GmbH
Braunschweig
1
--
--
--
Veränderung der Landnutzung in der nord-westlichen Uckermark von 1780 bis heute
Vielfalt in der Uckermark : Forschungsprojekte 2015 - 2018
false
true
Lina Weiß
Monika Wulff
Geowissenschaften
Institut für Biochemie und Biologie
62367
2019
2019
deu
62
book
oerding print GmbH
Braunschweig
1
--
--
--
Vielfalt in der Uckermark
Forschungsprojekte 2015 - 2018
Bundesministerium für Bildung und Forschung
Deutsche Forschungsgemeinschaft
false
true
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
62202
2023
2023
eng
155
doctoralthesis
1
--
--
2023-12-18
Mobile link functions in unpredictable agricultural landscapes
Animal movement is a crucial aspect of life, influencing ecological and evolutionary processes. It plays an important role in shaping biodiversity patterns, connecting habitats and ecosystems. Anthropogenic landscape changes, such as in agricultural environments, can impede the movement of animals by affecting their ability to locate resources during recurring movements within home ranges and, on a larger scale, disrupt migration or dispersal. Inevitably, these changes in movement behavior have far-reaching consequences on the mobile link functions provided by species inhabiting such extensively altered matrix areas. In this thesis, I investigate the movement characteristics and activity patterns of the European hare (Lepus europaeus), aiming to understand their significance as a pivotal species in fragmented agricultural landscapes. I reveal intriguing results that shed light on the importance of hares for seed dispersal, the influence of personality traits on behavior and space use, the sensitivity of hares to extreme weather conditions, and the impacts of GPS collaring on mammals' activity patterns and movement behavior.
In Chapter I, I conducted a controlled feeding experiment to investigate the potential impact of hares on seed dispersal. By additionally utilizing GPS data of hares in two contrasting landscapes, I demonstrated that hares play a vital role, acting as effective mobile linkers for many plant species in small and isolated habitat patches. The analysis of seed intake and germination success revealed that distinct seed traits, such as density, surface area, and shape, profoundly affect hares' ability to disperse seeds through endozoochory. These findings highlight the interplay between hares and plant communities and thus provide valuable insights into seed dispersal mechanisms in fragmented landscapes.
By employing standardized behavioral tests in Chapter II, I revealed consistent behavioral responses among captive hares while simultaneously examining the intricate connection between personality traits and spatial patterns within wild hare populations. This analysis provides insights into the ecological interactions and dynamics within hare populations in agricultural habitats. Examining the concept of animal personality, I established a link between personality traits and hare behavior. I showed that boldness, measured through standardized tests, influences individual exploration styles, with shy and bold hares exhibiting distinct space use patterns. In addition to providing valuable insights into the role of animal personality in heterogeneous environments, my research introduced a novel approach demonstrating the feasibility of remotely assessing personality types using animal-borne sensors without additional disturbance of the focal individual.
While climate conditions severely impact the activity and, consequently, the fitness of wildlife species across the globe, in Chapter III, I uncovered the sensitivity of hares to temperature, humidity, and wind speed during their peak reproduction period. I found a strong response in activity to high temperatures above 25°C, with a particularly pronounced effect during temperature extremes of over 35°C. The non-linear relationship between temperature and activity was characterized by contrasting responses observed for day and night. These findings emphasize the vulnerability of hares to climate change and the potential consequences for their fitness and population dynamics with the ongoing rise of temperature.
Since such insights can only be obtained through capturing and tagging free-ranging animals, I assessed potential impacts and the recovery process post-collar attachment in Chapter IV. For this purpose, I examined the daily distances moved and the temporal-associated activity of 1451 terrestrial mammals out of 42 species during their initial tracking period. The disturbance intensity and the speed of recovery varied across species, with herbivores, females, and individuals captured and collared in relatively secluded study areas experiencing more pronounced disturbances due to limited anthropogenic influences.
Mobile linkers are essential for maintaining biodiversity as they influence the dynamics and resilience of ecosystems. Furthermore, their ability to move through fragmented landscapes makes them a key component for restoring disturbed sites. Individual movement decisions determine the scale of mobile links, and understanding variations in space use among individuals is crucial for interpreting their functions. Climate change poses further challenges, with wildlife species expected to adjust their behavior, especially in response to high-temperature extremes, and comprehending the anthropogenic influence on animal movements will remain paramount to effective land use planning and the development of successful conservation strategies.
This thesis provides a comprehensive ecological understanding of hares in agricultural landscapes. My research findings underscore the importance of hares as mobile linkers, the influence of personality traits on behavior and spatial patterns, the vulnerability of hares to extreme weather conditions, and the immediate consequences of collar attachment on mammalian movements. Thus, I contribute valuable insights to wildlife conservation and management efforts, aiding in developing strategies to mitigate the impact of environmental changes on hare populations. Moreover, these findings enable the development of methodologies aimed at minimizing the impacts of collaring while also identifying potential biases in the data, thereby benefiting both animal welfare and the scientific integrity of localization studies.
Die Bewegung von Tieren ist ein entscheidender Aspekt des Lebens, der ökologische und evolutionäre Prozesse beeinflusst. Sie spielt eine wichtige Rolle bei der Gestaltung der biologischen Vielfalt und verbindet Lebensräume und Ökosysteme miteinander. Anthropogene Landschaftsveränderungen, z.B. in der Landwirtschaft, können die Bewegung von Tieren behindern, indem sie ihre Fähigkeiten beeinträchtigen, Ressourcen innerhalb ihres täglichen Bewegungsradius zu lokalisieren und im größeren Maßstab, ihre Wanderung oder Ausbreitung limitieren. In dieser Thesis untersuche ich die Bewegungsmerkmale und Aktivitätsmuster des Feldhasen (Lepus europaeus), um seine Bedeutung als Schlüsselart in fragmentierten Agrarlandschaften zu verstehen. Ich lege faszinierende Ergebnisse vor, die die Bedeutung des Hasen für die Verbreitung von Saatgut, den Einfluss von Persönlichkeitsmerkmalen auf das Verhalten und die Raumnutzung, die Sensibilität des Hasen gegenüber extremen Witterungsbedingungen und die Auswirkungen von GPS-Empfängern auf die Aktivitätsmuster und das Bewegungsverhalten der Säugetiere beleuchten.
In Kapitel I führte ich ein kontrolliertes Fütterungsexperiment durch, um den potenziellen Einfluss von Hasen auf die Samenausbreitung zu analysieren. Durch die zusätzliche Verwendung von GPS-Daten von Hasen in zwei kontrastierenden Landschaften konnte ich nachweisen, dass Hasen eine wichtige Rolle spielen, da sie in kleinen und isolierten Habitatfeldern als effektive mobile Verbindungsglieder für viele Pflanzenarten fungieren. Die Analyse der Samenaufnahme und des Keimungserfolgs zeigte, dass verschiedene Eigenschaften der Samen, wie Dichte, Oberfläche und Form, die Fähigkeit der Hasen, Samen durch Endozoochorie zu verbreiten, stark beeinflussen. Diese Ergebnisse verdeutlichen die Wechselwirkung zwischen Hasen und Pflanzengemeinschaften und liefern somit wertvolle Erkenntnisse über die Mechanismen der Samenverbreitung in fragmentierten Landschaften.
Durch den Einsatz standardisierter Verhaltenstests in Kapitel II konnte ich konsistente Verhaltensreaktionen bei in Gefangenschaft lebenden Hasen aufdecken und zeitgleich den komplexen Zusammenhang zwischen Persönlichkeitsmerkmalen und räumlichen Mustern in Wildhasenpopulationen untersuchen. Diese Analyse bietet Einblicke in die ökologischen Interaktionen und die Dynamik von Hasenpopulationen in landwirtschaftlichen Lebensräumen. Indem ich das Konzept der Tierpersönlichkeit untersuchte, stellte ich eine Verbindung zwischen Persönlichkeitsmerkmalen und dem Verhalten von Hasen her. Ich habe gezeigt, dass die durch standardisierte Tests gemessene Kühnheit den individuellen Erkundungsstil beeinflusst, wobei schüchterne und kühne Hasen unterschiedliche Raumnutzungsmuster aufweisen. Meine Forschung liefert nicht nur wertvolle Einblicke in die Rolle der Tierpersönlichkeit in heterogenen Umgebungen, sondern stellt auch einen neuartigen Ansatz vor, der die Durchführbarkeit einer Fernbeurteilung von Persönlichkeitstypen mithilfe von am Tier angebrachten Sensoren ohne zusätzliche Störung des Zielindividuums demonstrierte.
Da die Klimabedingungen die Aktivität und folglich die Fitness von Wildtierarten auf der ganzen Welt stark beeinflussen, habe ich in Kapitel III die Sensibilität von Hasen gegenüber Temperatur, Luftfeuchtigkeit und Windgeschwindigkeit während ihrer Hauptfortpflanzungszeit ermittelt. Ich stellte fest, dass die Aktivität stark auf hohe Temperaturen über 25 °C reagiert, wobei die Auswirkungen bei extremen Temperaturen von über 35 °C besonders ausgeprägt sind. Die nicht lineare Beziehung zwischen Temperatur und Aktivität war durch gegensätzliche Reaktionen bei Tag und Nacht gekennzeichnet. Diese Ergebnisse unterstreichen die Anfälligkeit der Hasen für den Klimawandel und die möglichen Folgen für ihre Fitness und Populationsdynamik bei einem anhaltenden Temperaturanstieg.
Da solche Erkenntnisse nur durch Fangen und Besendern von Wildtieren ermöglicht werden können, habe ich in Kapitel IV die potenziellen negativen Auswirkungen auf das Individuuum, sowie den Erholungsprozess nach dem Anlegen des Halsbandes untersucht. Hierfür analysierte ich die zurückgelegten täglichen Entfernungen in Verbindung mit der Aktivität von 1451 terrestrischen Säugetieren aus 42 verschiedenen Arten während ihrer anfänglichen Verfolgung. Die Intensität der Störung sowie die Geschwindigkeit der Erholung variieren je nach Art, wobei Pflanzenfresser, Weibchen und Individuen, die in relativ abgelegenen Untersuchungsgebieten gefangen und mit Halsbändern versehen wurden, aufgrund bisher begrenzter anthropogener Einflüsse stärkere Störungen erfahren.
Mobile Verbindungsglieder sind essentiell für die Erhaltung der Biodiversität, indem sie eine wichtige Rolle in der Dynamik und Resilienz von Ökosystemen spielen. Weiterhin macht ihre Fähigkeit, sich durch zerstückelte Landschaften zu bewegen sie zu wichtigen Schlüsselkomponenten bei der Wiederherstellung von zerstörten Landschaften. Individuelle Bewegungsentscheidungen bestimmen den Maßstab der mobilen Verbindungen und die Schwankungen der Raumnutzung unter Individuen zu verstehen ist unerlässlich, um deren Funktion zu interpretieren. Der Klimawandel stellt eine weitere Herausforderung dar, indem Wildtiere dazu gezwungen werden, sich zu adaptieren, insbesondere an Hochtemperatur-Extreme. Den anthropogenen Einfluss auf Tierbewegungen aufzudecken bleibt von größter Bedeutung in der Landnutzungsplanung und die Entwicklung von erfolgreichen Strategien zum Schutz der Natur.
Diese Thesis liefert ein umfassendes ökologisches Verständnis von Feldhasen in Agrarlandschaften. Die Ergebnisse meiner Forschung unterstreichen die Bedeutung von Hasen als mobile Bindeglieder, den Einfluss von Persönlichkeitsmerkmalen auf Verhalten und räumliche Muster, die Anfälligkeit von Hasen gegenüber extremen Wetterbedingungen und die unmittelbaren Folgen der Halsbandanbringung auf Tierbewegungen. Damit leiste ich einen wertvollen Beitrag zum Schutz und zur Bewirtschaftung von Wildtieren, indem ich die Entwicklung von Strategien zur Abschwächung der Auswirkungen von Umweltveränderungen auf Hasenpopulationen unterstütze. Darüber hinaus ermöglichen diese Erkenntnisse die Entwicklung von Methoden, die darauf abzielen, die Folgen der Halsbandanbringung zu minimieren und gleichzeitig potenzielle Verzerrungen in den Daten zu identifizieren, was sowohl dem Tierschutz als auch der wissenschaftlichen Integrität von Lokalisierungsstudien zugutekommt.
10.25932/publishup-62202
urn:nbn:de:kobv:517-opus4-622023
online registration
publish
Dissertation, Universität Potsdam, 2023
WT 3531, RB 10513
CC-BY - Namensnennung 4.0 International
Jonas Stiegler
eng
uncontrolled
European hare
eng
uncontrolled
mammals
eng
uncontrolled
ecology
eng
uncontrolled
animal personality
eng
uncontrolled
seed dispersal
eng
uncontrolled
movement ecology
eng
uncontrolled
tracking impacts
eng
uncontrolled
energy budget
eng
uncontrolled
climate change
eng
uncontrolled
accelerometry
eng
uncontrolled
GPS
eng
uncontrolled
tracking
deu
uncontrolled
Feldhase
deu
uncontrolled
GPS
deu
uncontrolled
Beschleunigungsmessungen
deu
uncontrolled
Tierpersönlichkeit
deu
uncontrolled
Klimawandel
deu
uncontrolled
Tierökologie
deu
uncontrolled
Energiebudget
deu
uncontrolled
Säugetiere
deu
uncontrolled
Bewegungsökologie
deu
uncontrolled
Samenausbreitung
deu
uncontrolled
Tierortung
deu
uncontrolled
Konsequenzen von Fang und Besenderung
Biowissenschaften; Biologie
open_access
Institut für Biochemie und Biologie
Universität Potsdam
Universität Potsdam
https://publishup.uni-potsdam.de/files/62202/stiegler_diss.pdf
62354
2022
eng
14
19
43
article
Wiley-VCH
Weinheim
1
2022-06-10
2022-06-10
--
Antimicrobial polymers of linear and bottlebrush architecture
Polymeric antimicrobial peptide mimics are a promising alternative for the future management of the daunting problems associated with antimicrobial resistance. However, the development of successful antimicrobial polymers (APs) requires careful control of factors such as amphiphilic balance, molecular weight, dispersity, sequence, and architecture. While most of the earlier developed APs focus on random linear copolymers, the development of APs with advanced architectures proves to be more potent. It is recently developed multivalent bottlebrush APs with improved antibacterial and hemocompatibility profiles, outperforming their linear counterparts. Understanding the rationale behind the outstanding biological activity of these newly developed antimicrobials is vital to further improving their performance. This work investigates the physicochemical properties governing the differences in activity between linear and bottlebrush architectures using various spectroscopic and microscopic techniques. Linear copolymers are more solvated, thermo-responsive, and possess facial amphiphilicity resulting in random aggregations when interacting with liposomes mimicking Escheria coli membranes. The bottlebrush copolymers adopt a more stable secondary conformation in aqueous solution in comparison to linear copolymers, conferring rapid and more specific binding mechanism to membranes. The advantageous physicochemical properties of the bottlebrush topology seem to be a determinant factor in the activity of these promising APs.
Macromolecular rapid communications : publishing the newsletters of the European Polymer Federation
Probing the membrane interaction and physicochemical properties
35686622
1521-3927
10.1002/marc.202200288
1022-1336
outputup:dataSource:WoS:2022
2200288
WOS:000815016100001
Hartlieb, Matthias (corresponding author), Univ Potsdam, Inst Chem, Karl Liebknecht Str 24, D-14476 Potsdam, Germany.; Hartlieb, M (corresponding author), Fraunhofer Inst Appl Polymer Res IAP, Geiselbergstr 69, D-14476 Potsdam, Germany., mhartlieb@uni-potsdam.de
DFG (Emmy-Noether-Program) [HA 7725/2-1]; NGO forderverein Uni Kinshasa; e. V.; Else-Kroener-Fresenius Stiftung; Holger-Poehlmann Foundation;; Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) [EXC; 2008 - 390540038 - UniSysCat]; DFG [406260942]; Projekt DEAL
Hartlieb, Matthias
2024-01-29T13:20:04+00:00
sword
importub
filename=package.tar
df27efc60eaba713845c3f9ddbb7aacd
1475027-2
CC-BY-NC - Namensnennung, nicht kommerziell 4.0 International
Alain Murhimalika Bapolisi
Patrycja Kielb
Marek Bekir
Anne-Catherine Lehnen
Christin Radon
Sophie Laroque
Petra Wendler
Henrike Müller-Werkmeister
Matthias Hartlieb
eng
uncontrolled
antimicrobial polymers
eng
uncontrolled
bottlebrush copolymers
eng
uncontrolled
liposomes
eng
uncontrolled
membrane
eng
uncontrolled
interactions
eng
uncontrolled
quartz crystal microbalance
Chemie und zugeordnete Wissenschaften
Institut für Physik und Astronomie
Institut für Chemie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
62345
2022
2022
eng
13
6
34
article
Wiley
Hoboken
1
2022-02-18
2022-02-18
--
Development of birthweight and length for gestational age and sex references in Yucatan, Mexico
Objective To develop sex- and gestational age specific reference percentiles and curves for birth weight and length for Yucatec neonates using data from birth registers of infants born during 2015-2019. Material and methods Observational, descriptive, epidemiologic study in a 5-year period including every registered birth in the state of Yucatan, Mexico using birth registries. A total of 158 432 live, physically healthy singletons (76 442 females and 81 990 males) between 25 and 42 weeks of gestation were included in the analysis. We used the LMS method to construct smoothed reference centiles (3rd, 10th, 25th, 50th, 75th, 95th, and 97th) and curves for males and females separately. Results Mean maternal age was 26 (SD = 6.22) years. Fifty-two percent of births occurred by vaginal delivery, 37% were firstborn and similar proportions were second (33%) and third or more (30%) born. 5.5% of newborns included in the references corresponds to neonates born before 37 weeks of gestation (5.9% boys and 5.1% girls). In both sexes, the percentage of infants with a birthweight less than 2500 g was 6.7%. The birthweight at the 50th percentile for males and females at 40 weeks of gestation in this cohort was 3256 and 3167 g, respectively, and the corresponding values for birth length were 50.23 and 49.84 cm (mean differences between sexes: 89 g and 0.40 cm, respectively). Conclusion The reference percentile and curves developed in this study are useful for research purposes and can help health practitioners to assess the biological status of infants born in Yucatan.
American journal of human biology : the official journal of the Human Biology Council
10.1002/ajhb.23732
35179265
1042-0533
1520-6300
outputup:dataSource:WoS:2022
e23732
WOS:000757458000001
Azcorra, H (corresponding author), Univ Modelo, Ctr Invest Silvio Zavala, Carretera Cholul 200 Metros Perifer Norte, Merida 97310, Yucatan, Mexico.; Mendez-Dominguez, N (corresponding author), Hosp Reg Alta Especialidad Peninsula Yucatan, Subdirecc Ensenanza & Invest, Calle 7 433 X 20 Y 22 Fracc Altabrisa, Merida 97139, Yucatan, Mexico., hugoazpe@hotmail.com; ninamendezdominguez@gmail.com
Azcorra, Hugo
2024-01-29T11:09:25+00:00
sword
importub
filename=package.tar
1e5d1dbad108addb1838d779b80c6c59
1025339-7
false
true
CC-BY - Namensnennung 4.0 International
Hugo Azcorra
Federico Dickinson
Nina Mendez-Dominguez
Rebekka Mumm
Graciela Valentín
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
62343
2022
2022
eng
9
1977
289
article
Royal Society
London
1
2022-06-22
2022-06-22
--
Evolution of toxins as a public good in phytoplankton
Toxic phytoplankton blooms have increased in many waterbodies worldwide with well-known negative impacts on human health, fisheries and ecosystems. However, why and how phytoplankton evolved toxin production is still a puzzling question, given that the producer that pays the costs often shares the benefit with other competing algae and thus provides toxins as a 'public good' (e.g. damaging a common competitor or predator). Furthermore, blooming phytoplankton species often show a high intraspecific variation in toxicity and we lack an understanding of what drives the dynamics of coexisting toxic and non-toxic genotypes. Here, by using an individual-based two-dimensional model, we show that small-scale patchiness of phytoplankton strains caused by demography can explain toxin evolution in phytoplankton with low motility and the maintenance of genetic diversity within their blooms. This patchiness vanishes for phytoplankton with high diffusive motility, suggesting different evolutionary pathways for different phytoplankton groups. In conclusion, our study reveals that small-scale spatial heterogeneity, generated by cell division and counteracted by diffusive cell motility and turbulence, can crucially affect toxin evolution and eco-evolutionary dynamics in toxic phytoplankton species. This contributes to a better understanding of conditions favouring toxin production and the evolution of public goods in asexually reproducing organisms in general.
Proceedings of the Royal Society of London : B, Biological sciences
10.1098/rspb.2022.0393
35730156
0962-8452
1471-2954
outputup:dataSource:WoS:2022
20220393
WOS:000814354000003
Ehrlich, E (corresponding author), Univ Potsdam, Inst Biochem & Biol, Dept Ecol & Ecosyst Modelling, Am Neuen Palais 10, D-14469 Potsdam, Germany.; Ehrlich, E (corresponding author), Leibniz Inst Freshwater Ecol & Inland Fisheries, Dept Fish Biol Fisheries & Aquaculture, Muggelseedamm 310, D-12587 Berlin, Germany., elias.ehrlich@igb-berlin.de
Ehrlich, Elias
2024-01-29T10:38:42+00:00
sword
importub
filename=package.tar
968b07067d3c1c080badcd0a88c36fb7
209242-6
1460975-7
Elias Ehrlich
Uffe Høgsbro Thygesen
Thomas Kiørboe
eng
uncontrolled
toxic algal blooms
eng
uncontrolled
evolution of cooperation
eng
uncontrolled
coexistence
eng
uncontrolled
patchiness in
eng
uncontrolled
phytoplankton
eng
uncontrolled
eco-evolutionary feedback
eng
uncontrolled
spatial pattern formation
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
62333
2022
2022
eng
3
16
14
1
25
article
Wiley-Blackwell
Oxford [u.a.]
1
2021-10-28
2022-10-28
--
Top-down effects of foraging decisions on local, landscape and regional biodiversity of resources (DivGUD)
Foraging by consumers acts as a biotic filtering mechanism for biodiversity at the trophic level of resources. Variation in foraging behaviour has cascading effects on abundance, diversity, and functional trait composition of the community of resource species. Here we propose diversity at giving-up density (DivGUD), i.e. when foragers quit exploiting a patch, as a novel concept and simple measure quantifying cascading effects at multiple spatial scales. In experimental landscapes with an assemblage of plant seeds, patch residency of wild rodents decreased local alpha-DivGUD (via elevated mortality of species with large seeds) and regional gamma-DivGUD, while dissimilarity among patches in a landscape (beta-DivGUD) increased. By linking theories of adaptive foraging behaviour with community ecology, DivGUD allows to investigate cascading indirect predation effects, e.g. the ecology-of-fear framework, feedbacks between functional trait composition of resource species and consumer communities, and effects of inter-individual differences among foragers on the biodiversity of resource communities.
Ecology letters
10.1111/ele.13901
34713543
1461-0248
outputup:dataSource:PubMed:2022
WOS:000712100200001
Eccard, Jana (corresponding author), Univ Potsdam, Inst Biochem & Biol, Anim Ecol, Maulbeerallee 1, D-14469 Potsdam, Germany., eccard@uni-potsdam.de
German Research FoundationGerman Research Foundation (DFG)
Eccard, Jana
2024-01-29T07:24:19+00:00
sword
importub
filename=package.tar
b4cc9180fa747fd94f1c832b6df15d19
2020195-3
false
true
CC-BY-NC-ND - Namensnennung, nicht kommerziell, keine Bearbeitungen 4.0 International
Jana Eccard
Clara Mendes Ferreira
Andres Peredo Arce
Melanie Dammhahn
eng
uncontrolled
biodiversity
eng
uncontrolled
cascading effects
eng
uncontrolled
foraging behaviour
eng
uncontrolled
functional traits
eng
uncontrolled
giving-up density
eng
uncontrolled
landscape of fear
eng
uncontrolled
optimal foraging
eng
uncontrolled
patch use
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
62337
2022
2022
eng
1144
1160
17
4
234
article
Wiley
Hoboken
1
2022-01-17
2022-01-17
--
Epigenetic regulation of thermomorphogenesis and heat stress tolerance
Many environmental conditions fluctuate and organisms need to respond effectively. This is especially true for temperature cues that can change in minutes to seasons and often follow a diurnal rhythm. Plants cannot migrate and most cannot regulate their temperature. Therefore, a broad array of responses have evolved to deal with temperature cues from freezing to heat stress. A particular response to mildly elevated temperatures is called thermomorphogenesis, a suite of morphological adaptations that includes thermonasty, formation of thin leaves and elongation growth of petioles and hypocotyl. Thermomorphogenesis allows for optimal performance in suboptimal temperature conditions by enhancing the cooling capacity. When temperatures rise further, heat stress tolerance mechanisms can be induced that enable the plant to survive the stressful temperature, which typically comprises cellular protection mechanisms and memory thereof. Induction of thermomorphogenesis, heat stress tolerance and stress memory depend on gene expression regulation, governed by diverse epigenetic processes. In this Tansley review we update on the current knowledge of epigenetic regulation of heat stress tolerance and elevated temperature signalling and response, with a focus on thermomorphogenesis regulation and heat stress memory. In particular we highlight the emerging role of H3K4 methylation marks in diverse temperature signalling pathways.
New phytologist : international journal of plant science
10.1111/nph.17970
35037247
0028-646X
1469-8137
outputup:dataSource:WoS:2022
WOS:000751510500001
van Zanten, M (corresponding author), Univ Utrecht, Inst Environm Biol, Mol Plant Physiol, Padualaan 8, NL-3584 CH Utrecht, Netherlands., m.vanzanten@uu.nl
European Research Council [ERC CoG 725295]
van Zanten, Martijn
2024-01-29T08:53:10+00:00
sword
importub
filename=package.tar
8e2339698b1d3a2223e1d22a55dbee60
1472194-6
208885-X
Giorgio Perrella
Isabel Bäurle
Martijn van Zanten
eng
uncontrolled
chromatin remodelling
eng
uncontrolled
elevated temperature
eng
uncontrolled
epigenetics
eng
uncontrolled
heat stress
eng
uncontrolled
histone modification
eng
uncontrolled
memory
eng
uncontrolled
temperature response
eng
uncontrolled
thermomorphogenesis
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
62334
2022
2022
eng
12
1
10
article
BMC
London
1
2022-03-26
2022-03-26
--
The plant microbiota signature of the Anthropocene as a challenge for microbiome research
Background:
One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene.
Results:
Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies.
Conclusions:
Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health.
Microbiome
10.1186/s40168-021-01224-5
35346369
2049-2618
outputup:dataSource:WoS:2022
54
WOS:000773956100001
Berg, G (corresponding author), Graz Univ Technol, Inst Environm Biotechnol, Petersgasse 12, A-8010 Graz, Austria.; Berg, G (corresponding author), Leibniz Inst Agr Engn Potsdam, Max Eyth Allee 100, D-14469 Potsdam, Germany.; Berg, G (corresponding author), Univ Potsdam, Inst Biochem & Biol, Karl Liebknecht Str 24-25, D-14476 Potsdam, Germany., Gabriele.berg@tugraz.at
Berg, Gabriele
2024-01-29T08:12:47+00:00
sword
importub
filename=package.tar
ecae00c2b1a73d0d31484148ab7378dd
2697425-3
false
true
CC-BY - Namensnennung 4.0 International
Gabriele Berg
Tomislav Cernava
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
61528
2022
2022
eng
11900
11973
74
14
122
article
American Chemical Society
Washington, DC
1
2022-07-18
2022-07-18
--
Second and outer coordination sphere effects in nitrogenase, hydrogenase, formate dehydrogenase, and CO dehydrogenase
Gases like H-2, N-2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N-2, CO2, and CO and the production of H-2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N-2 fixation by nitrogenase and H-2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
Chemical reviews : CR
10.1021/acs.chemrev.1c00914
35849738
0009-2665
1520-6890
outputup:dataSource:PubMed:2022
WOS:000893823900001
Stripp, ST (corresponding author), Free Univ Berlin, Expt Mol Biophys, D-14195 Berlin, Germany., sven.stripp@gmail.com
Deutsche Forschungsgemeinschaft (DFG) [SPP 1927, STR1554/5-1,; E1171-15-2]; Centre National de la Recherche Scientifique (CNRS), Aix; Marseille Universite; Agence Nationale de la Recherche; [ANR-11-BSV5-0005, ANR-12BS08-0014, ANR-14-CE05-0010, ANR-15-CE05-0020,; ANR16-CE29-0010, ANR-17-CE11-0027, ANR-18-CE05-0029]; Excellence; Initiative of Aix-Marseille University A*MIDEX, a French; "Investissements d'Avenir" programme [ANR-11-IDEX-0001-02]; Germany 's; Excellence Strategy [EXC 2008/1, EXC 2008-390540038]; Japan Society for; the Promotion of Science (JSPS) [JP21H02060, JP20H03215]; NIH-NIGMS; grants [GM67626, GM141046]; Department of Energy grants DOE (BES); [DE-SC0016510, DE-SC0014470]; NSF [CHE-1904131, CHE-1651398]; U.S.; Department of Energy (DOE) [DE-SC0016510, DE-SC0014470] Funding Source:; U.S. Department of Energy (DOE); Agence Nationale de la Recherche (ANR); [ANR-11-BSV5-0005, ANR-17-CE11-0027] Funding Source: Agence Nationale de; la Recherche (ANR)
Stripp, Sven T.
2023-11-23T06:19:41+00:00
sword
importub
filename=package.tar
35488b356f1e558d6afd0ffbfc14c158
2003609-7
207949-5
false
true
Sven T. Stripp
Benjamin R. Duffus
Vincent Fourmond
Christophe Leger
Silke Leimkühler
Shun Hirota
Yilin Hu
Andrew Jasniewski
Hideaki Ogata
Markus W. Ribbe
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
62315
2022
2022
eng
10
68
article
Elsevier
London
1
2022-05-27
2022-08-01
--
Recent advances in understanding thermomorphogenesis signaling
Plants show remarkable phenotypic plasticity and are able to adjust their morphology and development to diverse environmental stimuli. Morphological acclimation responses to elevated ambient temperatures are collectively termed thermomorphogenesis. In Arabidopsis thaliana, morphological changes are coordinated to a large extent by the transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), which in turn is regulated by several thermosensing mechanisms and modulators. Here, we review recent advances in the identification of factors that regulate thermomorphogenesis of Arabidopsis seedlings by affecting PIF4 expression and PIF4 activity. We summarize newly identified thermosensing mechanisms and highlight work on the emerging topic of organ- and tissue-specificity in the regulation of thermomorphogenesis.
Current opinion in plant biology
10.1016/j.pbi.2022.102231
35636376
1369-5266
1879-0356
outputup:dataSource:WoS:2022
102231
WOS:000821311600008
Delker, Carolin (corresponding author), Martin Luther Univ Halle Wittenberg, Inst Agr & Nutr Sci, Betty Heimann Str 5, D-06120 Halle, Germany.; Wigge, Philip Anthony (corresponding author), Leibniz Inst Gemuse & Zierpflanzenbau, Grossbeeren, Germany.; Wigge, PA (corresponding author), Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany., carolin.delker@landw.uni-halle.de; wigge@igzev.de
DFG [Qu 141/10-1, Qu 141/3-2]; European Research Council [Adv; 101021246]; Leibniz Association
Wigge, Philip Anthony
2024-01-25T14:04:15+00:00
sword
importub
filename=package.tar
2bd5ae9af3da0a084e87d10e2e2e9e00
Delker, Carolin
2019227-7
1418472-2
CC-BY - Namensnennung 4.0 International
Carolin Delker
Marcel Quint
Philip Anthony Wigge
Pflanzen (Botanik)
Institut für Biochemie und Biologie
Referiert
Import
Hybrid Open-Access
62303
2022
2022
eng
12
4
14
article
MDPI
Basel
1
2022-04-16
2022-04-16
--
Factors of detection deficits in vascular plant inventories - an island case study
The degree of completeness of large-scale floristic inventories is often difficult to judge. We compared prior vascular plant species inventories of the Mediterranean island of Limnos (North Aegean, Greece) with 231 recent records from 2016-2021. Together with the recent records, the known number of vascular plant species on the island is 960 native taxa, 63 established neophytes, and 27 species of as yet casual status for a total of 1050 taxa. We looked at a number of traits (plant family, size, flower color, perceptibility, habitat, reproduction period, rarity, and status) to investigate whether they were overrepresented in the dataset of the newly found taxa. Overrepresentation was found in some plant families (e.g., Poaceae and Chenopodiaceae) and for traits such as hydrophytic life form, unobtrusive flower color, coastal as well as agricultural and ruderal habitats, and late (summer/autumn) reproduction period. Apart from the well-known fact of esthetic bias, we found evidence for ecological and perceptibility biases. Plant species inventories based on prior piecemeal collated data should focus on regionally specific species groups and underrepresented and rare habitats.
Diversity
10.3390/d14040303
1424-2818
outputup:dataSource:WoS:2022
303
WOS:000786967500001
Panitsa, M (corresponding author), Univ Patras, Dept Biol, Div Plant Biol, Lab Bot, Panepistimiopolis 26504, Rio, Greece., michael.ristow@uni-potsdam.de; mpanitsa@upatras.gr; smeyerl@gwdg.de; <br /> erwin.bergmeier@bio.uni-goettingen.de
MAVA; Fondation pour la Nature
Panitsa, Maria
2024-01-25T11:32:31+00:00
sword
importub
filename=package.tar
9927661f520687ce927f2a6c825a2172
2518137-3
CC-BY - Namensnennung 4.0 International
Michael Ristow
Maria Panitsa
Stefan Meyer
Erwin Bergmeier
eng
uncontrolled
Aegean flora
eng
uncontrolled
floristic survey
eng
uncontrolled
Mediterranean island
eng
uncontrolled
perceptibility
eng
uncontrolled
habitat
eng
uncontrolled
plant traits
eng
uncontrolled
rarity
Naturwissenschaften und Mathematik
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62302
2022
2022
eng
8
1
12
article
Springer
Heidelberg
1
2022-05-23
2022-05-23
--
Does the cytokine adsorber CytoSorb (R) reduce vancomycin exposure in critically ill patients with sepsis or septic shock?
Background:
Hemadsorption of cytokines is used in critically ill patients with sepsis or septic shock. Concerns have been raised that the cytokine adsorber CytoSorb (R) unintentionally adsorbs vancomycin. This study aimed to quantify vancomycin elimination by CytoSorb (R) .
Methods:
Critically ill patients with sepsis or septic shock receiving continuous renal replacement therapy and CytoSorb (R) treatment during a prospective observational study were included in the analysis. Vancomycin pharmacokinetics was characterized using population pharmacokinetic modeling. Adsorption of vancomycin by the CytoSorb (R) was investigated as linear or saturable process. The final model was used to derive dosing recommendations based on stochastic simulations.
Results:
20 CytoSorb (R) treatments in 7 patients (160 serum samples/24 during CytoSorb (R)-treatment, all continuous infusion) were included in the study. A classical one-compartment model, including effluent flow rate of the continuous hemodialysis as linear covariate on clearance, best described the measured concentrations (without CytoSorb (R)). Significant adsorption with a linear decrease during CytoSorb (R) treatment was identified (p <0.0001) and revealed a maximum increase in vancomycin clearance of 291% (initially after CytoSorb (R) installation) and a maximum adsorption capacity of 572 mg. For a representative patient of our cohort a reduction of the area under the curve (AUC) by 93 mg/L*24 h during CytoSorb (R) treatment was observed. The additional administration of 500 mg vancomycin over 2 h during CytoSorb (R) attenuated the effect and revealed a negligible reduction of the AUC by 4 mg/L*24h.
Conclusion:
We recommend the infusion of 500 mg vancomycin over 2 h during CytoSorb (R) treatment to avoid subtherapeutic concentrations.
Annals of intensive care
a prospective observational study
10.1186/s13613-022-01017-5
35599248
2110-5820
outputup:dataSource:WoS:2022
44
WOS:000798594900001
Liebchen, Uwe (corresponding author), Ludwig Maximilians Univ Munchen, Univ Hosp, Dept Anesthesiol, Marchioninistr 15, D-81377 Munich, Germany.; Liebchen, U (corresponding author), Free Univ Berlin, Inst Pharm, Dept Clin Pharm & Biochem, Kelchstr 31, D-12169 Berlin, Germany., uwe.liebchen@med.uni-muenchen.de
Projekt DEAL; Munich Clinician-Scientist Program; Medical Faculty of the; LMU Munich [002]
Liebchen, Uwe
2024-01-25T11:11:19+00:00
sword
importub
filename=package.tar
763788a39666f326e684b89062613e4a
2617094-2
false
true
CC-BY - Namensnennung 4.0 International
Christina Scharf
Ferdinand Anton Weinelt
Ines Schroeder
Michael Paal
Michael Weigand
Michael Zoller
Michael Irlbeck
Charlotte Kloft
Josef Briegel
Uwe Liebchen
eng
uncontrolled
Vancomycin
eng
uncontrolled
Critically ill patients
eng
uncontrolled
CytoSorb (R)
eng
uncontrolled
Sepsis;
eng
uncontrolled
Pharmacokinetics
eng
uncontrolled
Adsorption
Medizin und Gesundheit
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62286
2021
2021
eng
16
135
article
Elsevier
Amsterdam
1
2021-12-28
2021-12-28
--
A new protocol for estimation of woody aboveground biomass in disturbance-prone ecosystems
Almost one third of global drylands are open forests and savannas, which are typically shaped by frequent natural disturbances such as wildfire and herbivory. Studies on ecosystem functions and services of woody vegetation require robust estimates of aboveground biomass (AGB). However, most methods have been developed for comparatively undisturbed forest ecosystems. As they are not tailored to accurately quantify AGB of small and irregular growth forms, their application on these growth forms may lead to unreliable or even biased AGB estimates in disturbance-prone dryland ecosystems. Moreover, these methods cannot quantify AGB losses caused by disturbance agents. Here we propose a methodology to estimate individual-and stand-level woody AGB in disturbance-prone ecosystems. It consists of flexible field sampling routines and estimation workflows for six growth classes, delineated by size and damage criteria. It also comprises a detailed damage assessment, harnessing the ecological archive of woody growth for past disturbances.
Based on large inventories collected along steep gradients of elephant disturbances in African dryland ecosystems, we compared the AGB estimates generated with our proposed method against estimates from a less adapted forest inventory method. We evaluated the necessary stepwise procedures of method adaptation and analyzed each step's effect on stand-level AGB estimation. We further explored additional advantages of our proposed method with regard to disturbance impact quantification. Results indicate that a majority of growth forms and individuals in savanna vegetation could only be assessed if methods of AGB estimation were adapted to the conditions of a disturbance-prone ecosystem. Furthermore, our damage assessment demonstrated that one third to half of all woody AGB was lost to disturbances. Consequently, less adapted methods may be insufficient and are likely to render inaccurate AGB estimations.
Our proposed method has the potential to accurately quantify woody AGB in disturbance-prone ecosystems, as well as AGB losses. Our method is more time consuming than conventional allometric approaches, yet it can cover sufficient areas within reasonable timespans, and can also be easily adapted to alternative sampling schemes.
Ecological indicators : integrating monitoring, assessment and management
10.1016/j.ecolind.2021.108466
1470-160X
1872-7034
outputup:dataSource:WoS:2022
108466
WOS:000761393800005
Kindermann, L (corresponding author), Univ Potsdam, Fac Sci, Inst Biochem & Biol, Biodivers Res & Systemat Bot, D-14469 Potsdam, Germany., Liana.Kindermann@uni-potsdam.de
German Research Foundation (DFG) through the collaborative research; center "Future Rural Africa" [TRR 228/1]; DAAD Promos scholarships; German Federal Government (BMBF) through the WASCAL WRAP 2.0 initiative; [01LG2078A]
Kindermann, Liana
2024-01-25T06:55:28+00:00
sword
importub
filename=package.tar
2ff41ca7bb2786d2a3ca3a69d712bbe8
2063587-4
2036774-0
CC-BY-NC-ND - Namensnennung, nicht kommerziell, keine Bearbeitungen 4.0 International
Liana Kindermann
Magnus Dobler
Daniela Niedeggen
Anja Linstädter
eng
uncontrolled
Damage assessment
eng
uncontrolled
Disturbance impacts
eng
uncontrolled
Tree growth classes
eng
uncontrolled
Method
eng
uncontrolled
comparison
eng
uncontrolled
Flexible sampling strategy
eng
uncontrolled
Tree allometry
eng
uncontrolled
Woody
eng
uncontrolled
aboveground biomass
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62222
2021
2021
eng
6
3
23
article
Wiley-VCH
Weinheim
1
2021-12-01
2021-12-01
--
Tailoring enzyme stringency masks the multispecificity of a lyngbyatoxin (indolactam alkaloid) nonribosomal peptide synthetase
Indolactam alkaloids are activators of protein kinase C (PKC) and are of pharmacological interest for the treatment of pathologies involving PKC dysregulation. The marine cyanobacterial nonribosomal peptide synthetase (NRPS) pathway for lyngbyatoxin biosynthesis, which we previously expressed in E. coli, was studied for its amenability towards the biosynthesis of indolactam variants. Modification of culture conditions for our E. coli heterologous expression host and analysis of pathway products suggested the native lyngbyatoxin pathway NRPS does possess a degree of relaxed specificity. Site-directed mutagenesis of two positions within the adenylation domain (A-domain) substrate-binding pocket was performed, resulting in an alteration of substrate preference between valine, isoleucine, and leucine. We observed relative congruence of in vitro substrate activation by the LtxA NRPS to in vivo product formation. While there was a preference for isoleucine over leucine, the substitution of alternative tailoring domains may unveil the true in vivo effects of the mutations introduced herein.
ChemBioChem
10.1002/cbic.202100574
34850512
1439-4227
1439-7633
outputup:dataSource:PubMed:2022
WOS:000728729400001
Neilan, BA (corresponding author), Univ New South Wales, Sch Biotechnol & Biomol Sci, Sydney, NSW 2052, Australia.; Neilan, BA (corresponding author), Univ Newcastle, Sch Environm & Life Sci, Callaghan, NSW 2308, Australia., brett.neilan@newcastle.edu.au
Australian Research CouncilAustralian Research Council [LP140100642]; Australian Government RTP ScholarshipAustralian Government; Adrian Lee Travel Scholarship
Neilan, Brett A.
2024-01-22T06:42:45+00:00
sword
importub
filename=package.tar
074d4b6cac0796463fe4b5e88f1f5b24
2020469-3
2019276-9
false
true
Angela H. Soeriyadi
Sarah E. Ongley
Jan-Christoph Kehr
Russel Pickford
Elke Dittmann
Brett A. Neilan
eng
uncontrolled
a domain
eng
uncontrolled
indolactams
eng
uncontrolled
MbtH
eng
uncontrolled
natural products
eng
uncontrolled
teleocidin
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
62223
2021
2021
eng
1443
1452
10
10
44
article
Wiley-Blackwell
Oxford [u.a.]
1
2021-08-29
2021-10-22
--
RangeShiftR
Reliably modelling the demographic and distributional responses of a species to environmental changes can be crucial for successful conservation and management planning. Process-based models have the potential to achieve this goal, but so far they remain underused for predictions of species' distributions. Individual-based models offer the additional capability to model inter-individual variation and evolutionary dynamics and thus capture adaptive responses to environmental change. We present RangeShiftR, an R implementation of a flexible individual-based modelling platform which simulates eco-evolutionary dynamics in a spatially explicit way. The package provides flexible and fast simulations by making the software RangeShifter available for the widely used statistical programming platform R. The package features additional auxiliary functions to support model specification and analysis of results. We provide an outline of the package's functionality, describe the underlying model structure with its main components and present a short example. RangeShiftR offers substantial model complexity, especially for the demographic and dispersal processes. It comes with elaborate tutorials and comprehensive documentation to facilitate learning the software and provide help at all levels. As the core code is implemented in C++, the computations are fast. The complete source code is published under a public licence, making adaptations and contributions feasible. The RangeShiftR package facilitates the application of individual-based and mechanistic modelling to eco-evolutionary questions by operating a flexible and powerful simulation model from R. It allows effortless interoperation with existing packages to create streamlined workflows that can include data preparation, integrated model specification and results analysis. Moreover, the implementation in R strengthens the potential for coupling RangeShiftR with other models.
Ecography : pattern and diversity in ecology / Nordic Ecologic Society Oikos
an R package for individual-based simulation of spatial changes
10.1111/ecog.05689
1600-0587
outputup:dataSource:WoS:2021
WOS:000690827900001
Malchow, Anne-Kathleen (corresponding author), Univ Potsdam, Inst Biochem & Biol, Potsdam, Germany., malchow@uni-potsdam.de
Deutsche Forschungsgemeinschaft (DFG)German Research Foundation (DFG) [ZU 361/1-1]; Royal Society University Research FellowshipRoyal Society of London [UF160614]
2024-01-22T07:01:36+00:00
sword
importub
filename=package.tar
60da465dbe4f5188d3e855275806dc30
2024917-2
Malchow, Anne-Kathleen
Anne-Kathleen Malchow
Greta Bocedi
Stephen C. F. Palmer
Justin M. J. Travis
Damaris Zurell
eng
uncontrolled
connectivity
eng
uncontrolled
conservation
eng
uncontrolled
dispersal
eng
uncontrolled
evolution
eng
uncontrolled
population dynamics
eng
uncontrolled
range dynamics
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62224
2022
2022
eng
10
37
article
Elsevier
Amsterdam
1
2022-05-13
2022-05-13
--
Wind turbines without curtailment produce large numbers of bat fatalities throughout their lifetime
Bats are protected by national and international legislation in European countries, yet many species, particularly migratory aerial insectivores, collide with wind turbines which counteracts conservation efforts. Within the European Union it is legally required to curtail the operation of wind turbines at periods of high bat activity, yet this is not practiced at old wind turbines. Based on data from the national carcass repository in Germany and from our own carcass searches at a wind park with three turbines west of Berlin, we evaluated the magnitude of bat casualties at old, potentially poor-sited wind turbines operating without curtailment. We report 88 documented bat carcasses collected by various searchers over the 20-year operation period of this wind park from 2001 to 2021. Common noctule bats (Nyctalus noctula) and common pipistrelles (Pipistrellus pipistrellus) were most often found dead at these turbines. Our search campaign in August and September 2021 yielded a total of 18 carcasses. We estimated that at least 209 bats were likely killed during our field survey, yielding more than 70 casualties/wind turbine or 39 casualties/ MW in two months. Since our campaign covered only part of the migration season, we consider this value as an underestimate. The 20-year period of the wind park emphasises the substantial impact old turbines may have on bat individuals and populations when operating without curtailments. We call for reconsidering the operation procedures of old wind turbines to stop the continuous loss of bats in Germany and other countries where turbine curtailments are even less practiced than in Germany.
Global ecology and conservation
a call against ignorance and neglect
10.1016/j.gecco.2022.e02149
2351-9894
outputup:dataSource:WoS:2022
e02149
WOS:000802791100005
Voigt, CC (corresponding author), Leibniz Inst Zoo & Wildlife Res, Alfred-Kowalke-Str 17, D-10315 Berlin, Germany., voigt@izw-berlin.de
Open Access Fund of the Leibniz Association; IZW - Deutsche; Forschungsgemeinschaft (German Research Foundation) [491292795]
Voigt, Christian C.
2024-01-22T07:03:18+00:00
sword
importub
filename=package.tar
8ec4819496122896df10dcac94a1edd2
2814786-8
false
true
CC-BY - Namensnennung 4.0 International
Christian C. Voigt
Klara Kaiser
Samantha Look
Kristin Scharnweber
Carolin Scholz
eng
uncontrolled
green-green dilemma
eng
uncontrolled
wind energy bat conflict
eng
uncontrolled
wildlife casualties
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import
Gold Open-Access
DOAJ gelistet
62228
2022
2022
eng
12
82
article
Elsevier
Oxford
1
2022-06-10
2022-06-10
--
The relationship between early childhood teachers' instructional quality and children's mathematics development
This study examined how early childhood (EC) teachers' instructional quality predicted children's development in mathematics across two measurement occasions. Therefore, EC teachers' (n = 25) instructional quality was assessed using one standardized observation instrument covering both domain-specific and general aspects of instructional quality. Additionally, data on children's (n = 208) outcome in early number skills was collected applying a standardized test. Multilevel structural equation modeling was used accounting for nested data. Children's age and the average size of preschool groups were controlled for. Results revealed that EC teachers' instructional quality predicted children's development but was not associated with their initial achievement. The findings suggest that instruments covering domain-specific and general aspects might be helpful in order to measure EC teachers' instructional quality in mathematics and predict children's learning growth. Understanding the mechanisms between instructional quality and children's development may help EC teachers to enhance their math teaching in practice.
Learning and instruction : the journal of the European Association for Research on Learning and Instruction
10.1016/j.learninstruc.2022.101636
0959-4752
1873-3263
outputup:dataSource:WoS:2022
101636
WOS:000812171800001
Pohle, L (corresponding author), Humboldt Univ, Dept Educ Studies, Unter Linden 6, D- 10099 Berlin, Germany., lara.pohle@hu-berlin.de; georg.hosoya@fu-berlin.de; <br /> jennifer.pohle@uni-potsdam.de; lars.jenssen@hu-berlin.de
German Federal Ministry of Education and Research [FKZ: 01PK15003A-C];; KoKoHs (Modeling and Measuring Competencies in Higher Education; -Validation and Methodological Innovations)
Pohle, Lara
2024-01-22T08:14:30+00:00
sword
importub
filename=package.tar
9d2e5b79a64066c6915460fc65ca60a1
2011980-X
1080798-6
Lara Pohle
Georg Hosoya
Jennifer Pohle
Lars Meyer-Jenßen
eng
uncontrolled
Early childhood education
eng
uncontrolled
Early childhood teachers
eng
uncontrolled
Instructional
eng
uncontrolled
quality
eng
uncontrolled
Early mathematics development
Biowissenschaften; Biologie
Institut für Biochemie und Biologie
Referiert
Import